e10vq
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UNITED STATES SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549
FORM 10-Q
(Mark One)
     
þ   Quarterly Report Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934
For the quarterly period ended: December 31, 2009
OR
     
o   Transition Report Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934
For the transition period from                      to                     
Commission File Number 0-25434
BROOKS AUTOMATION, INC.
(Exact name of registrant as specified in its charter)
     
Delaware   04-3040660
     
(State or other jurisdiction of
incorporation or organization)
  (I.R.S. Employer
Identification No.)
15 Elizabeth Drive
Chelmsford, Massachusetts
(Address of principal executive offices)
 
01824
(Zip Code)
 
Registrant’s telephone number, including area code: (978) 262-2400
 
Indicate by check mark whether the registrant: (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes þ No o
Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files). Yes o No o
Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company. See the definitions of “large accelerated filer,” “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act. (Check one):
             
Large accelerated filer o   Accelerated filer þ   Non-accelerated filer o (Do not check if a smaller reporting company)   Smaller reporting company o
Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). Yes o No þ
APPLICABLE ONLY TO ISSUERS INVOLVED IN BANKRUPTCY PROCEDINGS DURING THE PRECEDING FIVE YEARS
Indicate by check mark whether the registrant has filed all documents and reports required to be filed by Section 12, 13 or 15(d) of the Securities Exchange Act of 1934 subsequent to the distribution of securities under a plan confirmed by a court. Yes o No o
Indicate the number of shares outstanding of each of the registrant’s classes of common stock, as of the latest practical date, January 29, 2010: Common stock, $0.01 par value 64,551,247 shares
 
 

 


 

BROOKS AUTOMATION, INC.
INDEX
         
    PAGE NUMBER  
       
       
    3  
    4  
    5  
    6  
    16  
    22  
    22  
       
    23  
    23  
    23  
    24  
 EX-31.01 Section 302 Certification of Chief Executive Officer
 EX-31.02 Section 302 Certification of Chief Financial Officer
 EX-32 Section 906 Certification of Chief Executive Officer and Chief Financial Officer

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PART I. FINANCIAL INFORMATION
Item 1. Consolidated Financial Statements
BROOKS AUTOMATION, INC.
CONSOLIDATED BALANCE SHEETS
(unaudited)
(In thousands, except share and per share data)
                 
    December 31,     September 30,  
    2009     2009  
Assets
               
Current assets
               
Cash and cash equivalents
  $ 47,164     $ 59,985  
Marketable securities
    38,038       28,046  
Accounts receivable, net
    53,193       38,428  
Insurance receivable for litigation
    204       120  
Inventories, net
    89,763       84,738  
Prepaid expenses and other current assets
    10,464       9,872  
 
           
Total current assets
    238,826       221,189  
Property, plant and equipment, net
    71,391       74,793  
Long-term marketable securities
    26,157       22,490  
Goodwill
    48,138       48,138  
Intangible assets, net
    13,133       14,081  
Equity investment in joint ventures
    29,362       29,470  
Other assets
    2,684       3,161  
 
           
Total assets
  $ 429,691     $ 413,322  
 
           
Liabilities and equity
               
Current liabilities
               
Accounts payable
  $ 46,243     $ 26,360  
Deferred revenue
    4,097       2,916  
Accrued warranty and retrofit costs
    5,734       5,698  
Accrued compensation and benefits
    10,370       14,317  
Accrued restructuring costs
    4,786       5,642  
Accrued income taxes payable
    2,925       2,686  
Accrued expenses and other current liabilities
    11,716       12,870  
 
           
Total current liabilities
    85,871       70,489  
Accrued long-term restructuring
    2,263       2,019  
Income taxes payable
    11,035       10,755  
Long-term pension liability
    8,070       7,913  
Other long-term liabilities
    2,625       2,523  
 
           
Total liabilities
    109,864       93,699  
 
           
Contingencies (Note 14)
               
Equity
               
Preferred stock, $0.01 par value, 1,000,000 shares authorized, no shares issued and outstanding
           
Common stock, $0.01 par value, 125,000,000 shares authorized, 78,013,116 shares issued and 64,551,247 shares outstanding at December 31, 2009, 77,883,173 shares issued and 64,421,304 shares outstanding at September 30, 2009
    780       779  
Additional paid-in capital
    1,798,235       1,795,619  
Accumulated other comprehensive income
    16,781       16,318  
Treasury stock at cost, 13,461,869 shares at December 31, 2009 and September 30, 2009
    (200,956 )     (200,956 )
Accumulated deficit
    (1,295,426 )     (1,292,631 )
 
           
Total Brooks Automation, Inc. stockholders’ equity
    319,414       319,129  
Noncontrolling interest in subsidiaries
    413       494  
 
           
Total equity
    319,827       319,623  
 
           
Total liabilities and equity
  $ 429,691     $ 413,322  
 
           
The accompanying notes are an integral part of these unaudited consolidated financial statements.

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BROOKS AUTOMATION, INC.
CONSOLIDATED STATEMENTS OF OPERATIONS
(unaudited)
(In thousands, except per share data)
                 
    Three months ended  
    December 31,  
    2009     2008  
Revenues
               
Product
  $ 91,521     $ 59,086  
Services
    14,676       14,360  
 
           
Total revenues
    106,197       73,446  
 
           
Cost of revenues
               
Product
    67,245       53,869  
Services
    12,706       13,189  
 
           
Total cost of revenues
    79,951       67,058  
 
           
Gross profit
    26,246       6,388  
 
           
Operating expenses
               
Research and development
    7,541       9,277  
Selling, general and administrative
    18,979       27,634  
Restructuring charges
    1,522       4,105  
 
           
Total operating expenses
    28,042       41,016  
 
           
Operating loss
    (1,796 )     (34,628 )
Interest income
    328       897  
Interest expense
    16       126  
Loss on investment
    191       1,185  
Other expense, net
    197       38  
 
           
Loss before income taxes and equity in earnings (losses) of joint ventures
    (1,872 )     (35,080 )
Income tax provision
    635       391  
 
           
Loss before equity in earnings (losses) of joint ventures
    (2,507 )     (35,471 )
Equity in earnings (losses) of joint ventures
    (370 )     301  
 
           
Net loss
  $ (2,877 )   $ (35,170 )
Add: Net loss attributable to noncontrolling interests
    82       87  
 
           
Net loss attributable to Brooks Automation, Inc.
  $ (2,795 )   $ (35,083 )
 
           
 
               
Basic net loss per share attributable to Brooks Automation, Inc. common stockholders
  $ (0.04 )   $ (0.56 )
 
           
Diluted net loss per share attributable to Brooks Automation, Inc. common stockholders
  $ (0.04 )   $ (0.56 )
 
           
Shares used in computing loss per share
               
Basic
    63,394       62,651  
Diluted
    63,394       62,651  
The accompanying notes are an integral part of these unaudited consolidated financial statements.

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BROOKS AUTOMATION, INC.
CONSOLIDATED STATEMENTS OF CASH FLOWS
(unaudited)
(In thousands)
                 
    Three months ended  
    December 31,  
    2009     2008  
Cash flows from operating activities
               
Net loss
  $ (2,877 )   $ (35,170 )
Adjustments to reconcile net loss to net cash provided by (used in) operating activities:
               
Depreciation and amortization
    4,794       8,380  
Stock-based compensation
    1,517       1,524  
Amortization of premium (discount) on marketable securities
    136       (34 )
Undistributed (earnings) losses of joint ventures
    370       (301 )
Gain on disposal of long-lived assets
          (8 )
Loss on investment
    191       1,185  
Changes in operating assets and liabilities, net of acquisitions and disposals:
               
Accounts receivable
    (14,759 )     26,330  
Inventories
    (5,163 )     (3,252 )
Prepaid expenses and other current assets
    (834 )     71  
Accounts payable
    19,902       (7,580 )
Deferred revenue
    1,199       (330 )
Accrued warranty and retrofit costs
    32       (237 )
Accrued compensation and benefits
    (2,834 )     (1,201 )
Accrued restructuring costs
    (605 )     890  
Accrued expenses and other
    413       (3,745 )
 
           
Net cash provided by (used in) operating activities
    1,482       (13,478 )
 
           
Cash flows from investing activities
               
Purchases of property, plant and equipment
    (461 )     (5,084 )
Purchases of marketable securities
    (43,983 )     (35,022 )
Sale/maturity of marketable securities
    29,853       22,533  
Proceeds from the sale of investment
    240        
 
           
Net cash used in investing activities
    (14,351 )     (17,573 )
 
           
Effects of exchange rate changes on cash and cash equivalents
    48       (1,118 )
 
           
Net decrease in cash and cash equivalents
    (12,821 )     (32,169 )
Cash and cash equivalents, beginning of period
    59,985       110,269  
 
           
Cash and cash equivalents, end of period
  $ 47,164     $ 78,100  
 
           
The accompanying notes are an integral part of these unaudited consolidated financial statements.

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BROOKS AUTOMATION, INC.
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS (unaudited)
1. Basis of Presentation
     The unaudited condensed consolidated financial statements of Brooks Automation, Inc. and its subsidiaries (“Brooks” or the “Company”) included herein have been prepared in accordance with generally accepted accounting principles. In the opinion of management, all material adjustments which are of a normal and recurring nature necessary for a fair presentation of the results for the periods presented have been reflected.
     Certain information and footnote disclosures normally included in the Company’s annual consolidated financial statements have been condensed or omitted and, accordingly, the accompanying financial information should be read in conjunction with the consolidated financial statements and notes thereto contained in the Company’s Annual Report on Form 10-K, filed with the United States Securities and Exchange Commission (the “SEC”) for the year ended September 30, 2009. Certain reclassifications have been made in the prior period consolidated financial statements to conform to the current presentation.
     We evaluated subsequent events through February 5, 2010, the date of financial statement issuance.
Recently Enacted Accounting Pronouncements
     In September 2006, the Financial Accounting Standards Board (“FASB”) issued authoritative guidance for Fair Value Measurements and Disclosures which defines fair value, establishes a framework for measuring fair value and expands disclosures about assets and liabilities measured at fair value in the financial statements. In February 2008, the FASB issued authoritative guidance which allows for the delay of the effective date for fair value measurements for one year for all non-financial assets and non-financial liabilities, except for items that are recognized or disclosed at fair value in the financial statements on a recurring basis (at least annually). In April 2009, the FASB issued additional authoritative guidance in determining whether a market is active or inactive, and whether a transaction is distressed, is applicable to all assets and liabilities (i.e. financial and non-financial) and will require enhanced disclosures. This standard was effective beginning with the Company’s fourth quarter of fiscal 2009. The measurement and disclosure requirements related to financial assets and financial liabilities were effective for the Company beginning on October 1, 2008. See Note 13. On October 1, 2009 the Company adopted the fair value measurement standard for all non-financial assets and non-financial liabilities, which had no impact on its financial position or results of operations.
     In December 2007, the FASB revised the authoritative guidance for Business Combinations, which significantly changes the accounting for business combinations in a number of areas including the treatment of contingent consideration, pre-acquisition contingencies, transaction costs, restructuring costs and income taxes. On October 1, 2009 the Company adopted this standard prospectively and will apply the standard to any business combination with an acquisition date after October 1, 2009.
     In December 2007, the FASB issued authoritative guidance regarding Consolidation, which establishes accounting and reporting standards for noncontrolling interests in a subsidiary and for the deconsolidation of a subsidiary. This standard clarifies that a noncontrolling interest in a subsidiary is an ownership interest in the consolidated entity that should be reported as equity in the consolidated financial statements. The amount of net income attributable to the noncontrolling interest will be included in consolidated net income on the face of the income statement. Further, it clarifies that changes in a parent’s ownership interest in a subsidiary that do not result in deconsolidation are equity transactions if the parent retains its controlling financial interest. In addition, this standard requires that a parent recognize a gain or loss in net income when a subsidiary is deconsolidated. On October 1, 2009 the Company adopted this standard retrospectively, which did not have a material impact on its financial position or results of operations.
     In April 2008, the FASB issued authoritative guidance regarding the determination of the useful life of intangible assets. This guidance amends the factors that should be considered in developing renewal or extension assumptions used to determine the useful life of a recognized intangible asset. It also improves the consistency between the useful

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life of a recognized intangible asset and the period of expected cash flows used to measure the fair value of the asset. On October 1, 2009 the Company adopted this standard, which had no impact on its financial position or results of operations.
     In June 2008, the FASB issued authoritative guidance regarding whether instruments granted in share-based payment transactions are participating securities, which classifies unvested share-based payment awards that contain nonforfeitable rights to dividends or dividend equivalents (whether paid or unpaid) as participating securities and requires them to be included in the computation of earnings per share pursuant to the two-class method. On October 1, 2009 the Company adopted this standard, which had no impact on its financial position or results of operations.
     In December 2008, the FASB issued authoritative guidance regarding Compensation — Retirement Benefits, which requires enhanced disclosures about the plan assets of a company’s defined benefit pension and other postretirement plans. The enhanced disclosures are intended to provide users of financial statements with a greater understanding of: (1) how investment allocation decisions are made, including the factors that are pertinent to an understanding of investment policies and strategies; (2) the major categories of plan assets; (3) the inputs and valuation techniques used to measure the fair value of plan assets; (4) the effect of fair value measurements using significant unobservable inputs (Level 3) on changes in plan assets for the period; and (5) significant concentrations of risk within plan assets. This standard will be effective for the Company for the fiscal year ending September 30, 2010. The Company is currently evaluating the potential impact of this guidance on its future disclosures.
     In June 2009, the FASB issued an amendment to the accounting and disclosure requirements for the consolidation of variable interest entities (VIEs), which requires a qualitative approach to identifying a controlling financial interest in a VIE, and requires ongoing assessment of whether an entity is a VIE and whether an interest in a VIE makes the holder the primary beneficiary of the VIE. This guidance is effective for fiscal years beginning after November 15, 2009. The Company is currently evaluating the potential impact of this standard on its financial position and results of operations.
     In September 2009, the FASB issued authoritative guidance on revenue arrangements with multiple deliverables. This guidance provides another alternative for establishing fair value for a deliverable. When vendor specific objective evidence or third-party evidence for deliverables in an arrangement cannot be determined, companies will be required to develop a best estimate of the selling price for separate deliverables and allocate arrangement consideration using the relative selling price method. This guidance is effective October 1, 2010, and early adoption is permitted. The Company is currently evaluating the potential impact of this guidance on its financial position and results of operations.
2. Stock Based Compensation
     The following table reflects compensation expense recorded during the three months ended December 31, 2009 and 2008 (in thousands):
                 
    Three months ended  
    December 31,  
    2009     2008  
Stock options
  $ 43     $ 133  
Restricted stock
    1,368       1,251  
Employee stock purchase plan
    106       140  
 
           
 
  $ 1,517     $ 1,524  
 
           
     The Company uses the Black-Scholes valuation model for estimating the fair value of the stock options granted. The fair value per share of restricted stock is equal to the number of shares granted and the excess of the quoted price of the Company’s common stock over the exercise price of the restricted stock on the date of grant. In addition, for stock-based awards where vesting is dependent upon achieving certain operating performance goals, the Company estimates the likelihood of achieving the performance goals. Actual results, and future changes in estimates, may differ substantially from the Company’s current estimates. Restricted stock with market-based vesting criteria is valued using a lattice model. For the three months ended December 31, 2009, the Company

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recorded $0.4 million of expense on stock-based awards that have performance goals which will vest in the Company’s second fiscal quarter of 2010.
Stock Option Activity
     The following table summarizes stock option activity for the three months ended December 31, 2009:
                                 
            Weighted-              
            Average     Weighted     Aggregate  
    Number of     Remaining     Average     Intrinsic Value  
    Options     Contractual Term     Exercise Price     (In Thousands)  
Outstanding at September 30, 2009
    1,189,897             $ 17.54          
Forfeited/expired
    (59,175 )             14.20          
 
                           
Outstanding at December 31, 2009
    1,130,722     1.3 years   $ 17.71     $ 28  
Vested and unvested expected to vest at December 31, 2009
    1,129,477     1.3 years   $ 17.72     $ 28  
Options exercisable at December 31, 2009
    1,105,722     1.3 years   $ 17.82     $ 28  
     The aggregate intrinsic value in the table above represents the total intrinsic value, based on the Company’s closing stock price of $8.58 as of December 31, 2009, which would have been received by the option holders had all option holders exercised their options as of that date.
     No stock options were granted during the three months ended December 31, 2009 and 2008. There were no stock option exercises in the three months ended December 31, 2009 and 2008. The total intrinsic value of options exercised during the three month period ended December 31, 2009 and 2008 was $0. The total cash received from employees as a result of employee stock option exercises during the three months ended December 31, 2009 and 2008 was $0.
     As of December 31, 2009 future compensation cost related to nonvested stock options is approximately $0.1 million and will be recognized over an estimated weighted average period of 0.8 years.
Restricted Stock Activity
     A summary of the status of the Company’s restricted stock as of December 31, 2009 and changes during the three months ended December 31, 2009 is as follows:
                 
    Three months ended  
    December 31, 2009  
            Weighted  
            Average  
            Grant-Date  
    Shares     Fair Value  
Outstanding at September 30, 2009
    1,162,086     $ 8.96  
Awards granted
    178,346       7.85  
Awards vested
    (206,458 )     8.49  
Awards canceled
    (9,388 )     6.70  
 
           
Outstanding at December 31, 2009
    1,124,586     $ 8.89  
     In November 2009, the Company’s Board of Directors (“Board”) approved the payment of performance based variable compensation awards to certain executive management employees related to fiscal year 2009 performance. The Board chose to pay these awards in fully vested shares of the Company’s common stock rather than cash. The Company granted 178,346 shares based on the closing share price as of November 13, 2009. The $1.4 million of compensation expense related to these awards was recorded during fiscal year 2009 as selling, general and administrative expense.
     The fair value of restricted stock awards vested during the three months ended December 31, 2009 was $1.8 million, which includes the $1.4 million of compensation expense related to the fiscal year 2009 variable compensation award. The fair value of restricted stock awards vested during the three months ended December 31, 2008 was $0.4 million.

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     As of December 31, 2009, the unrecognized compensation cost related to nonvested restricted stock is $4.3 million and will be recognized over an estimated weighted average amortization period of 1.1 years.
Employee Stock Purchase Plan
     There were no shares purchased under the employee stock purchase plan during the three months ended December 31, 2009 and 2008.
3. Goodwill
     The components of the Company’s goodwill by business segment at December 31, 2009 are as follows (in thousands):
                                         
    Critical     Systems     Global              
    Solutions     Solutions     Customer              
    Group     Group     Operations     Other     Total  
Gross goodwill
  $ 353,253     $ 151,184     $ 151,238     $ 7,421     $ 663,096  
Less: aggregate impairment charges recorded
    (305,115 )     (151,184 )     (151,238 )     (7,421 )     (614,958 )
 
                             
 
  $ 48,138     $     $     $     $ 48,138  
 
                             
     The Company did not have any adjustments to goodwill during the three months ended December 31, 2009.
     Components of the Company’s identifiable intangible assets are as follows (in thousands):
                                                 
    December 31, 2009     September 30, 2009  
            Accumulated     Net Book             Accumulated     Net Book  
    Cost     Amortization     Value     Cost     Amortization     Value  
Patents
  $ 6,915     $ 6,815     $ 100     $ 6,915     $ 6,812     $ 103  
Completed technology
    43,502       35,737       7,765       43,502       35,280       8,222  
Trademarks and trade names
    3,779       3,140       639       3,779       3,060       719  
Customer relationships
    18,860       14,231       4,629       18,860       13,823       5,037  
 
                                   
 
  $ 73,056     $ 59,923     $ 13,133     $ 73,056     $ 58,975     $ 14,081  
 
                                   
4. Income Taxes
     The Company recorded an income tax provision of $0.6 million for the first quarter of fiscal year 2010. This provision is substantially impacted by foreign taxes arising from the Company’s international sales mix. This provision is also attributable to U.S. Federal alternative minimum taxes and certain state income taxes.
     The Company is subject to U.S. federal income tax and various state, local and international income taxes in various jurisdictions. The amount of income taxes paid is subject to the Company’s interpretation of applicable tax laws in the jurisdictions in which it files. In the normal course of business, the Company is subject to examination by taxing authorities throughout the world. The Company has income tax audits in progress in various states in which it operates. In the Company’s U.S. and international jurisdictions, the years that may be examined vary, with the earliest tax year being 2003. Based on the outcome of these examinations, or the expiration of statutes of limitations for specific jurisdictions, it is reasonably possible that the related unrecognized tax benefits could change from those recorded in the Company’s statement of financial position. The Company anticipates that several of these audits may be finalized within the next 12 months. The Company currently anticipates that approximately $0.4 million will be realized in the fourth quarter of fiscal year 2010 as a result of the expiration of certain non-U.S. statute of limitations, all of which will impact the Company’s fiscal year 2010 effective tax rate.

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5. Earnings (Loss) per Share
     Below is a reconciliation of weighted average common shares outstanding for purposes of calculating basic and diluted earnings (loss) per share (in thousands):
                 
    Three months ended  
    December 31,  
    2009     2008  
Weighted average common shares outstanding used in computing basic earnings (loss) per share
    63,394       62,651  
Dilutive common stock options and restricted stock awards
           
 
           
Weighted average common shares outstanding for purposes of computing diluted earnings (loss) per share
    63,394       62,651  
 
           
     Approximately 1,161,000 and 1,670,000 options to purchase common stock and 926,000 and 875,000 shares of restricted stock were excluded from the computation of diluted earnings (loss) per share attributable to common stockholders for the three months ended December 31, 2009 and 2008, respectively, as their effect would be anti-dilutive.
6. Comprehensive Income (Loss)
     The calculation of the Company’s comprehensive income (loss) for the three months ended December 31, 2009 and 2008 is as follows (in thousands):
                 
    Three months ended  
    December 31,  
    2009     2008  
Net loss
  $ (2,877 )   $ (35,170 )
Change in cumulative translation adjustment
    701       3,037  
Unrealized gain (loss) on marketable securities
    (238 )     304  
 
           
Comprehensive loss
    (2,414 )     (31,829 )
Add: Comprehensive loss attributable to noncontrolling interests
    82       87  
 
           
Comprehensive loss attributable to Brooks Automation, Inc
  $ (2,332 )   $ (31,742 )
 
           
7. Segment Information
     The Company reports financial results in three segments: Critical Solutions Group; Systems Solutions Group; and Global Customer Operations. In the second quarter of fiscal 2009 the Company realigned its management structure and its underlying internal financial reporting structure. Segment disclosures for prior periods have been revised to reflect the new reporting structure. A description of segments is included in the Company’s Annual Report on Form 10-K for the fiscal year ended September 30, 2009.
     The Company evaluates performance and allocates resources based on revenues, operating income (loss) and returns on invested assets. Operating income (loss) for each segment includes selling, general and administrative expenses directly attributable to the segment. Other unallocated corporate expenses (primarily certain legal costs associated with the Company’s past equity incentive-related practices and costs to indemnify a former executive in connection with these matters), amortization of acquired intangible assets (excluding completed technology) and restructuring, goodwill, and long-lived asset impairment charges are excluded from the segments’ operating income (loss). The Company’s non-allocable overhead costs, which include various general and administrative expenses, are allocated among the segments based upon various cost drivers associated with the respective administrative function, including segment revenues, segment headcount, or an analysis of the segments that benefit from a specific administrative function. Segment assets exclude investments in joint ventures, marketable securities and cash equivalents.

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     Financial information for the Company’s business segments is as follows (in thousands):
                                 
    Critical     Systems     Global        
    Solutions     Solutions     Customer        
    Group     Group     Operations     Total  
Three months ended December 31, 2009
                               
Revenues
                               
Product
  $ 43,186     $ 47,099     $ 1,236     $ 91,521  
Services
                14,676       14,676  
 
                       
 
  $ 43,186     $ 47,099     $ 15,912     $ 106,197  
 
                       
Gross profit
  $ 15,777     $ 7,556     $ 2,913     $ 26,246  
Segment operating income (loss)
  $ 1,868     $ 318     $ (1,884 )   $ 302  
 
                               
Three months ended December 31, 2008
                               
Revenues
                               
Product
  $ 35,883     $ 22,636     $ 567     $ 59,086  
Services
                14,360       14,360  
 
                       
 
  $ 35,883     $ 22,636     $ 14,927     $ 73,446  
 
                       
Gross profit (loss)
  $ 6,738     $ (1,738 )   $ 1,388     $ 6,388  
Segment operating loss
  $ (9,005 )   $ (13,352 )   $ (4,483 )   $ (26,840 )
 
                               
Assets
                               
December 31, 2009
  $ 143,043     $ 83,365     $ 55,270     $ 281,678  
September 30, 2009
  $ 138,930     $ 70,537     $ 56,007     $ 265,474  
     A reconciliation of the Company’s reportable segment operating income (loss) to the corresponding consolidated amounts for the three month periods ended December 31, 2009 and 2008 is as follows (in thousands):
                 
    Three months ended  
    December 31,  
    2009     2008  
Segment operating income (loss)
  $ 302     $ (26,840 )
Other unallocated corporate expenses
    85       1,790  
Amortization of acquired intangible assets
    491       1,893  
Restructuring charges
    1,522       4,105  
 
           
Total operating loss
  $ (1,796 )   $ (34,628 )
 
           
     A reconciliation of the Company’s reportable segment assets to the corresponding consolidated amounts as of December 31, 2009 and September 30, 2009 is as follows (in thousands):
                 
    December 31,     September 30,  
    2009     2009  
Segment assets
  $ 281,678     $ 265,474  
Investments in cash equivalents, marketable securities, joint ventures, and other unallocated corporate net assets
    147,809       147,728  
Insurance receivable
    204       120  
 
           
Total assets
  $ 429,691     $ 413,322  
 
           
8. Restructuring-Related Charges and Accruals
     The Company recorded charges to operations of $1,522,000 in the three months ended December 31, 2009 which consisted of facility related restructuring costs of $1,338,000 and $184,000 of severance costs. The severance charges include $77,000 for the elimination of three positions in the Company’s Global Customer Operations segment and $107,000 to adjust severance provisions related to general corporate positions eliminated in prior periods.
     During the preparation of the Company’s financial statements for the three months ended December 31, 2009, the Company identified certain accounting errors in its prior period financial statements that, individually and in aggregate, are not material to its financial statements taken as a whole for any related prior periods. The errors were

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related to the present value discounting of multi-year facility related restructuring liabilities. The total amount of the adjustment of $1,221,000 was recorded as a restructuring cost for the three months ended December 31, 2009. In addition, the Company recorded $117,000 of facility related restructuring costs during the three months ended December 31, 2009 to amortize the deferred discount on multi-year facility restructuring liabilities.
     The Company recorded a charge to operations of $4,105,000 in the three months ended December 31, 2008. These charges primarily relate to severance costs of $4,071,000 for workforce reductions of 120 employees in operations, service and administrative functions across all the main geographies in which the Company operates. The restructuring charges by segment for the first quarter of fiscal year 2009 were: Global Customer Operations — $2.7 million, Critical Solutions Group — $0.6 million and Systems Solutions Group — $0.4 million. In addition, the Company incurred $0.4 million of restructuring charges that were related to general corporate functions that support all of its segments.
     The activity for the three months ended December 31, 2009 and 2008 related to the Company’s restructuring-related accruals is summarized below (in thousands):
                                 
    Activity — Three Months Ended December 31, 2009  
    Balance                     Balance  
    September 30,                     December 31,  
    2009     Expense     Utilization     2009  
Facilities and other
  $ 6,289     $ 1,338     $ (1,125 )   $ 6,502  
Workforce-related
    1,372       184       (1,009 )     547  
 
                       
 
  $ 7,661     $ 1,522     $ (2,134 )   $ 7,049  
 
                       
                                 
    Activity — Three Months Ended December 31, 2008  
    Balance                     Balance  
    September 30,                     December 31,  
    2008     Expense     Utilization     2008  
Facilities and other
  $ 9,658     $ 34     $ (1,041 )   $ 8,651  
Workforce-related
    3,005       4,071       (2,227 )     4,849  
 
                       
 
  $ 12,663     $ 4,105     $ (3,268 )   $ 13,500  
 
                       
     The Company expects the majority of the remaining severance costs totaling $547,000 will be paid over the next twelve months. The expected facilities costs, totaling $6,502,000, net of estimated sub-rental income, will be paid on leases that expire through September 2011.
9. Loss on Investment
     During the three months ended December 31, 2009, the Company recorded a charge of $0.2 million for the sale of its minority equity investment in a closely-held Swiss public company. During the three months ended December 31, 2008, the Company recorded a charge of $1.2 million to write-down this investment to market value as of December 31, 2008. As of December 31, 2009, the Company no longer has an equity investment in this entity.
10. Employee Benefit Plans
     In connection with the acquisition of Helix Technology Corporation (“Helix”) in October 2005, the Company assumed the responsibility for the Helix Employees’ Pension Plan (the “Plan”). The Company froze the benefit accruals and future participation in this plan as of October 31, 2006.
     The components of the Company’s net pension cost related to the Plan for the three months ended December 31, 2009 and 2008 is as follows (in thousands):
                 
    Three months ended  
    December 31,  
    2009     2008  
Service cost
  $ 25     $ 25  
Interest cost
    193       171  
Amortization of losses
    82        
Expected return on assets
    (151 )     (199 )
 
           
Net periodic pension (benefit) cost
  $ 149     $ (3 )
 
           

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11. Other Balance Sheet Information
     Components of other selected captions in the Consolidated Balance Sheets are as follows (in thousands):
                 
    December 31,     September 30,  
    2009     2009  
Accounts receivable
  $ 53,846     $ 39,147  
Less allowances
    653       719  
 
           
 
  $ 53,193     $ 38,428  
 
           
 
               
Inventories, net
               
Raw materials and purchased parts
  $ 66,491     $ 65,815  
Work-in-process
    16,771       13,588  
Finished goods
    6,501       5,335  
 
           
 
  $ 89,763     $ 84,738  
 
           
     The Company provides for the estimated cost of product warranties, primarily from historical information, at the time product revenue is recognized and retrofit accruals at the time retrofit programs are established. While the Company engages in extensive product quality programs and processes, including actively monitoring and evaluating the quality of its component suppliers, the Company’s warranty obligation is affected by product failure rates, utilization levels, material usage, service delivery costs incurred in correcting a product failure, and supplier warranties on parts delivered to the Company. Product warranty and retrofit activity on a gross basis for the three months ended December 31, 2009 and 2008 is as follows (in thousands):
                         
Activity — Three Months Ended December 31, 2009
Balance                   Balance
September 30,                   December 31,
2009   Accruals   Settlements   2009
$5,698
  $ 2,496     $ (2,460 )   $ 5,734  
                         
Activity — Three Months Ended December 31, 2008
Balance                   Balance
September 30,                   December 31,
2008   Accruals   Settlements   2008
$8,174
  $ 3,085     $ (3,321 )   $ 7,938  
12. Joint Ventures
     The Company participates in a 50% joint venture, ULVAC Cryogenics, Inc., or UCI, with ULVAC Corporation of Chigasaki, Japan. UCI manufactures and sells cryogenic vacuum pumps, principally to ULVAC Corporation. For the three months ended December 31, 2009 and 2008, the Company recorded income (loss) associated with UCI of ($0.1) million and $0.3 million, respectively. At December 31, 2009, the carrying value of UCI in the Company’s consolidated balance sheet was $26.6 million. For the three months ended December 31, 2009 and 2008, management fee payments received by the Company from UCI were $0.1 million and $0.2 million, respectively. For the three months ended December 31, 2009 and 2008, the Company incurred charges from UCI for products or services of $0.2 million and $0.3 million, respectively. At December 31, 2009 and September 30, 2009 the Company owed UCI $0.2 million in connection with accounts payable for unpaid products and services.
     The Company participates in a 50% joint venture with Yaskawa Electric Corporation (“Yaskawa”) to form a joint venture called Yaskawa Brooks Automation, Inc. (“YBA”) to exclusively market and sell Yaskawa’s semiconductor robotics products and Brooks’ automation hardware products to semiconductor customers in Japan. For the three months ended December 31, 2009 and 2008, the Company recorded income (loss) associated with YBA of ($0.2) and $0.0 million, respectively. At December 31, 2009, the carrying value of YBA in the Company’s consolidated balance sheet was $2.8 million. For the three months ended December 31, 2009 and 2008, revenues earned by the Company from YBA were $1.8 million and $1.7 million, respectively. The amount due from YBA included in accounts receivable at December 31, 2009 and September 30, 2009 was $2.2 million and $2.4 million, respectively. For the three months ended December 31, 2009 and 2008, the Company did not incur any charges from YBA for products or services. At December 31, 2009 and September 30, 2009 the Company did not owe YBA any amount in connection with accounts payable for unpaid products and services.

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     These investments are accounted for using the equity method. Under this method of accounting, the Company records in income its proportionate share of the earnings of the joint ventures with a corresponding increase in the carrying value of the investment.
13. Fair Value Measurements
     In September 2006, the FASB issued authoritative guidance for fair value measurements and disclosures, which defines fair value, establishes a framework for measuring fair value and expands the related disclosure requirements. This statement applies under other accounting pronouncements that require or permit fair value measurements. The statement indicates, among other things, that a fair value measurement assumes that the transaction to sell an asset or transfer a liability occurs in the principal market for the asset or liability or, in the absence of a principal market, the most advantageous market for the asset or liability. This guidance defines fair value based upon an exit price model.
     The FASB amended the fair value measurement guidance to exclude accounting for leases and its related interpretive accounting pronouncements that address leasing transactions; the delay of the effective date of the measurement application to fiscal years beginning after November 15, 2008 for all non-financial assets and non-financial liabilities that are recognized or disclosed at fair value in the financial statements on a nonrecurring basis; and the determination of whether a market is active or inactive, and whether a transaction is distressed, is applicable to all assets and liabilities (i.e. financial and nonfinancial) and will require enhanced disclosures.
     The Company adopted the fair value measurement guidance as of October 1, 2008, with the exception of the application of the statement to non-recurring non-financial assets and non-financial liabilities. The Company adopted the fair value measurement guidance for non-recurring non-financial assets and non-financial liabilities on October 1, 2009.
     The fair value measurement guidance also establishes a fair value hierarchy which requires an entity to maximize the use of observable inputs and minimize the use of unobservable inputs when measuring fair value. The standard describes three levels of inputs that may be used to measure fair value:
  Level 1     Quoted prices in active markets for identical assets or liabilities as of the reporting date. Active markets are those in which transactions for the asset and liability occur in sufficient frequency and volume to provide pricing information on an ongoing basis.
  Level 2    Observable inputs other than Level 1 prices, such as quoted prices for similar assets or liabilities; quoted prices in markets that are not active; or other inputs that are observable or can be corroborated by observable market data for substantially the full term of the assets or liabilities.
  Level 3    Unobservable inputs that are supported by little or no market activity and that are significant to the fair value of the assets or liabilities.
     Assets and liabilities of the Company measured at fair value on a recurring basis as of December 31, 2009, are summarized as follows (in thousands):
                                 
            Fair Value Measurements at Reporting Date Using  
            Quoted Prices in              
            Active Markets for     Significant Other     Significant  
    December 31,     Identical Assets     Observable Inputs     Unobservable Inputs  
Description   2009     (Level 1)     (Level 2)     (Level 3)  
Assets
                               
Cash Equivalents
  $ 24,656     $ 24,656     $     $  
Available-for-sale securities
    64,195       25,143       39,052        
 
                       
Total Assets
  $ 88,851     $ 49,799     $ 39,052     $  
 
                       

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Cash Equivalents
     Cash equivalents of $24.7 million, consisting of Money Market Funds, are classified within Level 1 of the fair value hierarchy because they are valued using quoted market prices in active markets.
Available-For-Sale Securities
     Available-for-sale securities of $25.1 million, consisting of highly rated Corporate Bonds, are classified within Level 1 of the fair value hierarchy because they are valued using quoted market prices in active markets of identical assets or liabilities. Available-for-sale securities of $39.1 million, consisting of Asset Backed Securities, Municipal Bonds, and Government Agencies are classified within Level 2 of the fair value hierarchy because they are valued using matrix pricing and benchmarking. Matrix pricing is a mathematical technique used to value securities by relying on the securities’ relationship to other benchmark quoted prices.
14. Contingencies
     On August 22, 2006, an action captioned as Mark Levy v. Robert J. Therrien and Brooks Automation, Inc., was filed in the United States District Court for the District of Delaware, seeking recovery, on behalf of Brooks, from Mr. Therrien (the Company’s former Chairman and CEO) under Section 16(b) of the Securities Exchange Act of 1934 for alleged “short-swing” profits earned by Mr. Therrien due to the loan and stock option exercise in November 1999, and a sale by Mr. Therrien of Brooks stock in March 2000. The complaint seeks disgorgement of all profits earned by Mr. Therrien on the transactions, attorneys’ fees and other expenses. On February 20, 2007, a second Section 16(b) action, concerning the same loan and stock option exercise in November 1999 discussed above and seeking the same remedy, was filed in the United States District Court of the District of Delaware, captioned Aron Rosenberg v. Robert J. Therrien and Brooks Automation, Inc. On April 4, 2007, the court issued an order consolidating the Levy and Rosenberg actions. On July 14, 2008, the court denied Mr. Therrien’s motion to dismiss this action. Discovery has commenced in this matter and is currently ongoing. It has been reported to the Company that the parties have reached an agreement in principle to settle this case, subject to the approval of the court and to the conclusion by the parties of necessary settlement processes and documents. Brooks is a nominal defendant in the consolidated action and any recovery in this action, less attorneys’ fees, would go to the Company.
15. Subsequent Event
     On February 3, 2010, the Company entered into an agreement to sell certain intellectual property assets associated with factory automated material handling systems for $7.9 million. Under the terms of the agreement Brooks will retain the rights to use this intellectual property to support its existing installed base of factory automated material handling systems. The Company will record a gain of approximately $7.8 million on this sale during its second quarter of fiscal year 2010. The Company will receive $7.7 million of the proceeds from the sale during the second quarter of fiscal year 2010, and expects to receive the balance of $0.2 million during the second half of fiscal year 2010.

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Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations
     Certain statements in this Quarterly Report on Form 10-Q constitute “forward-looking statements” which involve known risks, uncertainties and other factors which may cause the actual results, our performance or our achievements to be materially different from any future results, performance or achievements expressed or implied by such forward-looking statements. Such factors include the Risk Factors which are set forth in our Annual Report on Form 10-K and which are incorporated herein by reference. Precautionary statements made in our Annual Report on Form 10-K should be read as being applicable to all related forward-looking statements whenever they appear in this report.
Overview
     We are a leading provider of automation, vacuum and instrumentation solutions and are a highly valued business partner to original equipment manufacturers (OEM) and equipment users throughout the world. We serve markets where equipment productivity and availability is a critical factor for our customers’ success. Our largest served market is the semiconductor manufacturing industry, which represented 71% and 84% of our consolidated revenues for fiscal year 2009 and the first quarter of fiscal year 2010, respectively. We also provide unique solutions to customers in data storage, advanced display, analytical instruments and industrial markets. We develop and deliver differentiated solutions that range from proprietary products to highly respected manufacturing services.
     The demand for semiconductors and semiconductor manufacturing equipment is cyclical, resulting in periodic expansions and contractions. Demand for our products has been impacted by these cyclical industry conditions. During fiscal year 2006 and throughout most of fiscal year 2007, we benefited from an industry expansion. That cyclical expansion turned to a downturn in the fourth quarter of fiscal year 2007 that continued through the second quarter of fiscal year 2009. Our revenues for the second quarter of fiscal year 2009 were $37.3 million. Since that time, our revenues have significantly increased in each fiscal quarter. Revenue for the first quarter of fiscal year 2010 was $106.2 million.
     Throughout fiscal years 2008 and 2009, we implemented a number of cost reduction programs to align our cost structure with a reduced demand environment. From the end of fiscal year 2007 through the end of fiscal year 2009, we reduced our headcount by approximately 40% and closed redundant facilities. Our cost reduction efforts focused on actions that would decrease our overhead cost structure for the foreseeable future. Although we have added personnel in recent months, these additions were made primarily to address increased production requirements. We will continue to add personnel to address our increasing production levels. We do not intend to significantly increase our overhead structure as our revenues recover.
     In connection with our restructuring programs, we have realigned our management structure and our underlying internal financial reporting structure. Effective as of the beginning of our second quarter of 2009, we implemented a new internal reporting structure which includes three segments: Critical Solutions Group, Systems Solutions Group and Global Customer Operations. Financial results prior to this new management structure have been revised to reflect our current segment structure.
     The Critical Solutions Group segment provides a variety of products critical to technology equipment productivity and availability. Those products include robots and robotic modules for atmospheric and vacuum applications and cryogenic vacuum pumping, thermal management and vacuum measurement solutions used to create, measure and control critical process vacuum applications.
     The Systems Solutions Group segment provides a range of products and engineering and manufacturing services, which include our Extended Factory services. Our Extended Factory product line provides services to build equipment front-end modules and other subassemblies which enable our customers to effectively develop and source high quality, high reliability, process tools for semiconductor and adjacent market applications.
     The Global Customer Operations segment provides an extensive range of support services including on and off-site repair services, on and off-site diagnostic support services, and installation services to enable our customers to maximize process tool uptime and productivity. This segment also provides services and spare parts for our Automated Material Handling Systems (“AMHS”) product line. Revenues from the sales of spare parts that are not

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related to a repair or replacement transaction, or are not AMHS products, are included within the product revenues of the other operating segments.
     On February 3, 2010, we entered into an agreement to sell certain intellectual property assets associated with factory automated material handling systems for $7.9 million. Under the terms of the agreement we will retain the rights to use this intellectual property to support our existing installed base of factory automated material handling systems. We will record a gain of approximately $7.8 million on this sale during our second quarter of fiscal year 2010. We will receive $7.7 million of the proceeds from the sale during the second quarter of fiscal year 2010, and expect to receive the balance of $0.2 million during the second half of fiscal year 2010.
Three Months Ended December 31 2009, Compared to Three Months Ended December 31, 2008
Revenues
     We reported revenues of $106.2 million for the first quarter of fiscal year 2010, compared to $73.4 million in the same prior year period, a 44.6% increase. The total increase in revenues of $32.8 million impacted all of our operating segments. Our Critical Solutions Group segment revenues increased by $7.3 million, our System Solutions Group segment revenues increased by $24.5 million and our Global Customer Operations segment revenues increased by $1.0 million. These increases were primarily the result of increased volume shipments in response to increasing demand for semiconductor capital equipment.
     Our Critical Solutions Group segment reported revenues of $43.2 million for the first quarter of fiscal year 2010, an increase of 20.3% from $35.9 million in the same prior year period. This increase is primarily attributable to a higher volume of shipments to semiconductor capital equipment customers. This increase was partially offset by lower volume of shipments of $2.3 million to non-semiconductor markets served by this segment.
     Our System Solutions Group segment reported revenues of $47.1 million for the first quarter of fiscal year 2010, a 108.1% increase from $22.6 million in the same prior year period. This increase is attributable to increased demand for semiconductor capital equipment. Included within this segment is our Extended Factory product line. Revenue for our Extended Factory product line was substantially the largest contributor to increased revenues in this segment, increasing by $19.2 million for the first quarter of fiscal year 2010 as compared to the same prior year period.
     Our Global Customer Operations segment reported revenues of $15.9 million for first quarter of fiscal year 2010, a 6.6% increase from $14.9 million in the same prior year period. This increase is attributable to higher AMHS spare parts revenue of $0.7 million and higher service contract and repair revenues of $0.3 million. All service revenues included in our unaudited consolidated statements of operations, which include service contract and repair services, are related to our Global Customer Operations segment.
Gross Profit
     Gross margin dollars increased to $26.2 million for the first quarter of fiscal year 2010, an increase of 310.9% from $6.4 million for the same prior year period. This increase was attributable to higher revenues of $32.8 million, a $5.2 million reduction in charges for excess and obsolete inventory and $1.9 million of reduced amortization expense for completed technology intangible assets, due primarily to the impairment recorded for those assets during the second quarter of fiscal 2009. These decreases were partially offset by a less favorable product mix which reduced gross margin dollars by $4.6 million. Gross margin was reduced by $0.5 million and $2.3 million for the first quarter of fiscal years 2010 and 2009, respectively, for amortization of completed technology, which relates primarily to the acquisition of Helix Technology Corporation (“Helix”) in October 2005.
     Gross margin percentage increased to 24.7% for the first quarter of fiscal year 2010, compared to 8.7% for the same prior year period. This increase was primarily attributable to higher absorption of indirect factory overhead on higher revenues. Other factors increasing gross margin percentage include decreased charges for excess and obsolete inventory which increased gross margin percentage by 6.6%, and reduced amortization expense for completed technology intangible assets which increased gross margin percentage by 2.8%. These increases in gross margin percentage were partially offset by a less favorable product mix which reduced gross margin percentage by 4.3%.

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     Gross margin of our Critical Solutions Group segment increased to $15.8 million for the first quarter of fiscal year 2010, an increase of 134.1% from $6.7 million in the same prior year period. This increase was attributable to higher revenues of $7.3 million, reduced charges for excess and obsolete inventory of $1.7 million and reduced amortization expense of $0.6 million for completed technology intangible assets, due primarily to the impairment recorded for those assets during the second quarter of fiscal 2009. Gross margin for the first quarter of fiscal years 2010 and 2009 was reduced by $0.4 million and $1.0 million, respectively, for completed technology amortization related to the Helix acquisition. Gross margin percentage was 36.5% for the first quarter of fiscal year 2010 as compared to 18.8% in the same prior year period. This increase is primarily the result of higher absorption of indirect factory overhead on higher revenues. Other factors increasing gross margin percentage include decreased charges for excess and obsolete inventory which increased gross margin percentage by 4.7%, and reduced amortization expense for completed technology intangible assets which increased gross margin percentage by 1.9%.
     Gross margin of our Systems Solutions Group segment increased to $7.6 million for the first quarter of fiscal year 2010, an increase of 534.7% from a $1.7 million loss for the same prior year period. This increase was attributable to higher revenues of $24.5 million, decreased charges for excess and obsolete inventory of $3.1 million and $0.2 million of reduced amortization expense for completed technology intangible assets, due primarily to the impairment recorded for those assets during the second quarter of fiscal year 2009. Gross margin for the first quarter of fiscal 2009 was reduced by $0.2 million for completed technology amortization. Gross margin percentage increased to 16.0% for the first quarter of fiscal year 2010 as compared to (7.7)% in the same prior year period. This increase was primarily attributable to higher absorption of indirect factory overhead on higher revenues. Other factors increasing gross margin percentage include decreased charges for excess and obsolete inventory which increased gross margin percentage by 12.4% and reduced amortization expense for completed technology intangible assets, which increased gross margin percentage by 0.7%. These increases in gross margin percentage were partially offset by a less favorable product mix which reduced gross margin percentage by 9.7%. The less favorable product mix is attributable to a $19.2 million increase in Extended Factory product sales, which are less profitable than other products within this segment. Extended Factory product revenues were 65% of all sales within this segment for the first quarter of fiscal year 2010, and we expect this product will continue to generate a majority of the revenue for this segment in the near term.
     Gross margin of our Global Customer Operations segment increased to $2.9 million for the first quarter of fiscal year 2010, an increase of 109.8% from the $1.4 million in the same prior year period. The increase was attributable to reduced amortization expense of $1.1 million for completed technology intangible assets, due primarily to the impairment recorded for those assets during the second quarter of 2009, decreased charges for excess and obsolete inventory of $0.4 million and higher revenues of $1.0 million. Gross margin for the first quarter of fiscal years 2010 and 2009 was reduced by $0.1 million and $1.2 million, respectively, for completed technology amortization related to the Helix acquisition. Gross margin percentage was 18.3% for the first quarter of fiscal year 2010 as compared to 9.3% in the same prior year period. The increase in gross margin percentage was primarily attributable to reduced amortization expense for completed technology intangible assets which increased gross margin percentage by 7.4%, and decreased charges for excess and obsolete inventory which decreased gross margin percentage by 2.6%.
Research and Development
     Research and development, or R&D, expenses for the first quarter of fiscal year 2010 were $7.5 million, a decrease of $1.8 million, compared to $9.3 million in the same prior year period. This decrease is primarily related to lower labor related costs of $1.7 million associated with headcount reductions. Our headcount reductions were implemented to remove redundancies in our R&D infrastructure. We will continue to invest in R&D projects that enhance our product and service offerings.
Selling, General and Administrative
     Selling, general and administrative, or SG&A expenses were $19.0 million for the first quarter of fiscal year 2010, a decrease of $8.6 million compared to $27.6 million in the same prior year period. The decrease is primarily attributable to lower labor costs of $3.7 million as we reduced our headcount to align our SG&A resources with our new management structure, a $1.4 million reduction in amortization of intangible assets primarily due to the impairment of intangible assets recorded in our second quarter of fiscal year 2009 and a $1.9 million reduction in litigation costs. We settled our litigation matters with the SEC during fiscal year 2008. The total indemnification

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costs, net of insurance reimbursements, were $(0.1) million and $1.8 million for the first quarter of fiscal years 2010 and 2009, respectively.
Restructuring Charges
     We recorded a charge of $1.5 million for the first quarter of fiscal year 2010 which consisted of facility related restructuring costs of $1.3 million and $0.2 million of severance costs. These severance costs include $0.1 million for the elimination of 3 positions in our Global Customer Operations segment, and $0.1 million to adjust severance provisions related to general corporate positions eliminated in prior periods.
     During the preparation of our financial statements for the first quarter of fiscal year 2010, we identified certain accounting errors in our prior period financial statements that, individually and in aggregate, are not material to our financial statements taken as a whole for any related prior periods. The errors were related to the present value discounting of multi-year facility related restructuring liabilities. The total amount of the adjustment of $1.2 million was recorded as a restructuring cost for the first quarter of fiscal year 2010. In addition, we recorded $0.1 million of facility related restructuring costs the first quarter of fiscal year 2010 to amortize the deferred discount on multi-year facility restructuring liabilities.
     We recorded a charge of $4.1 million for the first quarter of fiscal year 2009 as an initial charge for our fiscal 2009 restructuring plan. This charge consisted of severance costs associated with workforce reductions of 120 employees in operations, service and administrative functions across all the main geographies in which we operate. The restructuring charges by segment for the first quarter of fiscal year 2009 were: Global Customer Operations — $2.7 million, Critical Solutions Group — $0.6 million and Systems Solutions Group — $0.4 million. In addition, we incurred $0.4 million of restructuring charges that were related to general corporate functions that support all of our segments.
Interest Income
     Interest income was $0.3 million for the first quarter of fiscal year 2010 as compared to $0.9 million for the same prior year period. Approximately $0.3 million of this decrease is due to lower investment balances, with the balance of the decrease attributable to lower interest rates on our investments.
Loss on Investment
     During the first quarter of fiscal year 2010, we recorded a charge of $0.2 million for the sale of our minority equity investment in a closely-held Swiss public company. During the first quarter of fiscal year 2009, we recorded a charge of $1.2 million to write down this investment to market value as of December 31, 2008. As of December 31, 2009, we no longer have an equity investment in this entity.
Other Expense, net
     Other expense, net of $0.2 million for the first quarter of fiscal year 2010 consists primarily of foreign exchange losses, offset partially by management fee income of $0.1 million. Other expense, net of $0.0 million for the first quarter of fiscal year 2009 consists of management fee income of $0.2 million which has been fully offset by foreign exchange losses.
Income Tax Provision
     We recorded an income tax provision of $0.6 million for the first quarter of fiscal year 2010 and an income tax provision of $0.4 million for the same prior year period. The provision for the first quarter of fiscal year 2010 is substantially impacted by foreign taxes arising from our international sales mix. This provision is also attributable to U.S. Federal alternative minimum taxes and certain state income taxes. The tax provision for the first quarter of fiscal year 2009 is principally attributable to taxes on foreign income and interest related to unrecognized tax benefits. We continued to provide a full valuation allowance for our net deferred tax assets at December 31, 2009, as we believe it is more likely than not that the future tax benefits from accumulated net operating losses and deferred taxes will not be realized.

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Equity in Earnings (Losses) of Joint Ventures
     Income (loss) associated with our 50% interest in ULVAC Cryogenics, Inc., a joint venture with ULVAC Corporation of Japan, was $(0.1) million for the first quarter of fiscal year 2010, compared to $0.3 million in the same prior year period. The income (loss) associated with our 50% interest in Yaskawa Brooks Automation, Inc., a joint venture with Yaskawa Electric Corporation of Japan was $(0.2) million for the first quarter of fiscal year 2010 as compared to $0.0 million in the same prior year period.
Liquidity and Capital Resources
     Our business is significantly dependent on capital expenditures by semiconductor manufacturers and OEMs that are, in turn, dependent on the current and anticipated market demand for semiconductors. Demand for semiconductors is cyclical and has historically experienced periodic downturns. This cyclicality makes estimates of future revenues, results of operations and net cash flows inherently uncertain.
     At December 31, 2009, we had cash, cash equivalents and marketable securities aggregating $111.4 million. This amount was comprised of $47.2 million of cash and cash equivalents, $38.0 million of investments in short-term marketable securities and $26.2 million of investments in long-term marketable securities.
     Cash and cash equivalents were $47.2 million at December 31, 2009, a decrease of $12.8 million from September 30, 2009. This decrease was primarily due to $14.1 million of purchases in marketable securities, net of maturities. This decrease was partially offset by $1.5 million of cash provided by operating activities.
     Cash provided by operating activities was $1.5 million for the first quarter of fiscal year 2010, and was comprised of a net loss of $2.9 million, which includes $7.0 million of net non-cash related charges such as $4.8 million of depreciation and amortization and $1.5 million of stock-based compensation. Further, cash provided by operations was reduced by net increases in working capital of $2.6 million, consisting primarily of $14.8 million of increases in accounts receivable and $5.2 million of increases in inventory. The increases in accounts receivable and inventory were caused by a 65.7% increase in revenues for the first quarter of fiscal year 2010 as compared to the fourth quarter of fiscal year 2009. Additionally, we paid approximately $3.0 million in annual incentive compensation payments during the first quarter of fiscal year 2010 related to the prior fiscal year. These increases in working capital were partially offset by $19.9 million of increases in accounts payable and $1.2 million of higher deferred revenues.
     Cash used in investing activities was $14.4 million for the first quarter of fiscal year 2010, and is principally comprised of net purchases of marketable securities of $14.1 million and $0.5 million of capital expenditures. These uses of cash were partially offset by $0.2 million of proceeds from our sale of a minority equity investment in a closely-held Swiss public company. Our capital expenditures for the first quarter of fiscal year 2009 were $5.1 million, including $3.0 million in expenditures related to our Oracle ERP implementation. We implemented the Oracle ERP system in most of our U.S. operations in July 2009. We are currently evaluating the timing and cost to implement this system in our international locations.
     At December 31, 2009, we had approximately $0.5 million of letters of credit outstanding.
     We believe that we have adequate resources to fund our currently planned working capital and capital expenditure requirements for the next twelve months. However, the cyclical nature of our served markets and uncertainty with the current global economic environment makes it difficult for us to predict future liquidity requirements with certainty. We may be unable to obtain any required additional financing on terms favorable to us, if at all. If adequate funds are not available on acceptable terms, we may be unable to successfully develop or enhance products, respond to competitive pressure or take advantage of acquisition opportunities, any of which could have a material adverse effect on our business.

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Recently Enacted Accounting Pronouncements
     In September 2006, the Financial Accounting Standards Board (“FASB”) issued authoritative guidance for Fair Value Measurements and Disclosures which defines fair value, establishes a framework for measuring fair value and expands disclosures about assets and liabilities measured at fair value in the financial statements. In February 2008, the FASB issued authoritative guidance which allows for the delay of the effective date for fair value measurements for one year for all non-financial assets and non-financial liabilities, except for items that are recognized or disclosed at fair value in the financial statements on a recurring basis (at least annually). In April 2009, the FASB issued additional authoritative guidance in determining whether a market is active or inactive, and whether a transaction is distressed, is applicable to all assets and liabilities (i.e. financial and non-financial) and will require enhanced disclosures. This standard was effective beginning with our fourth quarter of fiscal 2009. The measurement and disclosure requirements related to financial assets and financial liabilities were effective for us beginning on October 1, 2008. See Note 13. On October 1, 2009 we adopted the fair value measurement standard for all non-financial assets and non-financial liabilities, which had no impact on our financial position or results of operations.
     In December 2007, the FASB revised the authoritative guidance for Business Combinations, which significantly changes the accounting for business combinations in a number of areas including the treatment of contingent consideration, pre-acquisition contingencies, transaction costs, restructuring costs and income taxes. On October 1, 2009 we adopted this standard prospectively and will apply the standard to any business combination with an acquisition date after October 1, 2009.
     In December 2007, the FASB issued authoritative guidance regarding Consolidation, which establishes accounting and reporting standards for noncontrolling interests in a subsidiary and for the deconsolidation of a subsidiary. This standard clarifies that a noncontrolling interest in a subsidiary is an ownership interest in the consolidated entity that should be reported as equity in the consolidated financial statements. The amount of net income attributable to the noncontrolling interest will be included in consolidated net income on the face of the income statement. Further, it clarifies that changes in a parent’s ownership interest in a subsidiary that do not result in deconsolidation are equity transactions if the parent retains its controlling financial interest. In addition, this standard requires that a parent recognize a gain or loss in net income when a subsidiary is deconsolidated. On October 1, 2009 we adopted this standard retrospectively, which did not have a material impact on our financial position or results of operations.
     In April 2008, the FASB issued authoritative guidance regarding the determination of the useful life of intangible assets. This guidance amends the factors that should be considered in developing renewal or extension assumptions used to determine the useful life of a recognized intangible asset. It also improves the consistency between the useful life of a recognized intangible asset and the period of expected cash flows used to measure the fair value of the asset. On October 1, 2009 we adopted this standard, which had no impact on our financial position or results of operations.
     In June 2008, the FASB issued authoritative guidance regarding whether instruments granted in share-based payment transactions are participating securities, which classifies unvested share-based payment awards that contain nonforfeitable rights to dividends or dividend equivalents (whether paid or unpaid) as participating securities and requires them to be included in the computation of earnings per share pursuant to the two-class method. All prior-period earnings per share data presented are to be adjusted retrospectively (including interim financial statements, summaries of earnings, and selected financial data) to conform with the provisions of this guidance. On October 1, 2009 we adopted this standard, which had no impact on our financial position or results of operations.
     In December 2008, the FASB issued authoritative guidance regarding Compensation — Retirement Benefits, which requires enhanced disclosures about the plan assets of a company’s defined benefit pension and other postretirement plans. The enhanced disclosures are intended to provide users of financial statements with a greater understanding of: (1) how investment allocation decisions are made, including the factors that are pertinent to an understanding of investment policies and strategies; (2) the major categories of plan assets; (3) the inputs and valuation techniques used to measure the fair value of plan assets; (4) the effect of fair value measurements using significant unobservable inputs (Level 3) on changes in plan assets for the period; and (5) significant concentrations of risk within plan assets. This standard will be effective for us for the fiscal year ending September 30, 2010. We are currently evaluating the potential impact of this guidance on our future disclosures.
     In June 2009, the FASB issued an amendment to the accounting and disclosure requirements for the consolidation of variable interest entities (VIEs), which requires a qualitative approach to identifying a controlling financial

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interest in a VIE, and requires ongoing assessment of whether an entity is a VIE and whether an interest in a VIE makes the holder the primary beneficiary of the VIE. This guidance is effective for fiscal years beginning after November 15, 2009. We are currently evaluating the potential impact of this standard on our financial position and results of operations.
     In September 2009, the FASB issued authoritative guidance on revenue arrangements with multiple deliverables. This guidance provides another alternative for establishing fair value for a deliverable. When vendor specific objective evidence or third-party evidence for deliverables in an arrangement cannot be determined, companies will be required to develop a best estimate of the selling price for separate deliverables and allocate arrangement consideration using the relative selling price method. This guidance is effective October 1, 2010, and early adoption is permitted. We are currently evaluating the potential impact of this guidance on our financial position and results of operations.
Item 3. Quantitative and Qualitative Disclosure About Market Risk
     We are exposed to a variety of market risks, including changes in interest rates affecting the return on our cash and cash equivalents, short-term and long-term investments and fluctuations in foreign currency exchange rates.
Interest Rate Exposure
     As our cash and cash equivalents consist principally of money market securities, which are short-term in nature, our exposure to market risk related to interest rate fluctuations for these investments is not significant. Our short-term and long-term investments consist mostly of highly rated corporate debt securities, and as such, market risk to these investments is not significant. During the three months ended December 31, 2009, the unrealized loss on marketable securities was $51,000. A hypothetical 100 basis point change in interest rates would result in an annual change of approximately $1.2 million in interest income earned.
Currency Rate Exposure
     We have transactions and balances denominated in currencies other than the U.S. dollar. Most of these transactions or balances are denominated in Euros and a variety of Asian currencies. Sales in currencies other than the U.S. dollar were 18.0% of our total sales for the three months ended December 31, 2009. These foreign sales were made primarily by our foreign subsidiaries, which have cost structures that substantially align with the currency of sale.
     In the normal course of our business, we have short-term advances between our legal entities that are subject to foreign currency exposure. These short-term advances were approximately $13.4 million at December 31, 2009, and relate to the Euro and a variety of Asian currencies. A majority of our foreign currency loss of $0.2 million for the three months ended December 31, 2009 relates to the currency fluctuation on these advances between the time the transaction occurs and the ultimate settlement of the transaction. A hypothetical 10% change in foreign exchange rates at December 31, 2009 would result in a $1.3 million change in our net income (loss). We mitigate the impact of potential currency translation losses on these short-term inter company advances by the timely settlement of each transaction, generally within 30 days.
Item 4. Controls and Procedures
     Evaluation of Disclosure Controls and Procedures. As of the end of the period covered by this report, and pursuant to Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, the Company’s management, including our chief executive officer and chief financial officer has concluded that our disclosure controls and procedures are effective.
     Change in Internal Controls. There were no changes in our internal control over financial reporting that occurred during our most recent fiscal quarter that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

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PART II. OTHER INFORMATION
Item 1. Legal Proceedings
     On August 22, 2006, an action captioned as Mark Levy v. Robert J. Therrien and Brooks Automation, Inc., was filed in the United States District Court for the District of Delaware, seeking recovery, on behalf of Brooks, from Mr. Therrien (the Company’s former Chairman and CEO) under Section 16(b) of the Securities Exchange Act of 1934 for alleged “short-swing” profits earned by Mr. Therrien due to the loan and stock option exercise in November 1999, and a sale by Mr. Therrien of Brooks stock in March 2000. The complaint seeks disgorgement of all profits earned by Mr. Therrien on the transactions, attorneys’ fees and other expenses. On February 20, 2007, a second Section 16(b) action, concerning the same loan and stock option exercise in November 1999 discussed above and seeking the same remedy, was filed in the United States District Court of the District of Delaware, captioned Aron Rosenberg v. Robert J. Therrien and Brooks Automation, Inc. On April 4, 2007, the court issued an order consolidating the Levy and Rosenberg actions. On July 14, 2008, the court denied Mr. Therrien’s motion to dismiss this action. Discovery has commenced in this matter and is currently ongoing. It has been reported to us that the parties have reached an agreement in principle to settle this case, subject to the approval of the court and to the conclusion by the parties of necessary settlement processes and documents. Brooks is a nominal defendant in the consolidated action and any recovery in this action, less attorneys’ fees, would go to the Company.
Item 2. Unregistered Sales of Equity Securities and Use of Proceeds
     The following table provides information concerning shares of our Common Stock $0.01 par value purchased in connection with the forfeiture of shares to satisfy the employees’ obligations with respect to withholding taxes in connection with the vesting of shares of restricted stock during the three months ended December 31, 2009. These purchases were made pursuant to the Amended and Restated 2000 Equity Incentive Plan.
                                 
                            Maximum  
                            Number (or  
                            Approximate  
                    Total Number of     Dollar Value) of  
    Total             Shares Purchased as     Shares that May Yet  
    Number             Part of Publicly     be Purchased Under  
    of Shares     Average Price Paid     Announced Plans     the Plans or  
Period   Purchased     per Share     or Programs     Programs  
October 1 — 31, 2009
    1,146     $ 6.88       1,146     $  
November 1 — 30, 2009
    37,869       7.76       37,869        
December 1 — 31, 2009
                       
 
                       
Total
    39,015     $ 7.73       39,015     $  
 
                       
Item 6. Exhibits
     The following exhibits are included herein:
     
Exhibit No.   Description
31.01
  Rule 13a-14(a), 15d-14(a) Certification.
     
31.02
  Rule 13a-14(a), 15d-14(a) Certification.
     
32
  Section 1350 Certifications.

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SIGNATURES
     Pursuant to the requirements of the Securities Exchange Act of 1934, the Registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized.
         
  BROOKS AUTOMATION, INC.
 
 
DATE: February 5, 2010  /s/ Martin S. Headley    
  Martin S. Headley   
  Executive Vice President and Chief Financial Officer (Principal Financial Officer)   
         
DATE: February 5, 2010  /s/ Timothy S. Mathews    
  Timothy S. Mathews   
  Vice President and Corporate Controller
(Principal Accounting Officer) 
 

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EXHIBIT INDEX
     
Exhibit No.   Description
31.01
  Rule 13a-14(a), 15d-14(a) Certification.
     
31.02
  Rule 13a-14(a), 15d-14(a) Certification.
     
32
  Section 1350 Certifications.

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