e10vq

-----BEGIN PRIVACY-ENHANCED MESSAGE----- Proc-Type: 2001,MIC-CLEAR Originator-Name: webmaster@www.sec.gov Originator-Key-Asymmetric: MFgwCgYEVQgBAQICAf8DSgAwRwJAW2sNKK9AVtBzYZmr6aGjlWyK3XmZv3dTINen TWSM7vrzLADbmYQaionwg5sDW3P6oaM5D3tdezXMm7z1T+B+twIDAQAB MIC-Info: RSA-MD5,RSA, GfyZe0XLOYyy3ZtrzLegzKP3SohHFjyBBgXpg4/BCEZ4I8jflCM3K05CXTqVkEpd n86dv/0drXBJg4g+M7grjA== 0000950135-09-000787.txt : 20090209 0000950135-09-000787.hdr.sgml : 20090209 20090209154539 ACCESSION NUMBER: 0000950135-09-000787 CONFORMED SUBMISSION TYPE: 10-Q PUBLIC DOCUMENT COUNT: 5 CONFORMED PERIOD OF REPORT: 20081231 FILED AS OF DATE: 20090209 DATE AS OF CHANGE: 20090209 FILER: COMPANY DATA: COMPANY CONFORMED NAME: BROOKS AUTOMATION INC CENTRAL INDEX KEY: 0000933974 STANDARD INDUSTRIAL CLASSIFICATION: SPECIAL INDUSTRY MACHINERY, NEC [3559] IRS NUMBER: 043040660 STATE OF INCORPORATION: DE FISCAL YEAR END: 0930 FILING VALUES: FORM TYPE: 10-Q SEC ACT: 1934 Act SEC FILE NUMBER: 000-25434 FILM NUMBER: 09581215 BUSINESS ADDRESS: STREET 1: 15 ELIZABETH DRIVE CITY: CHELMSFORD STATE: MA ZIP: 01824 BUSINESS PHONE: (978) 262-2400 MAIL ADDRESS: STREET 1: 15 ELIZABETH DRIVE CITY: CHELMSFORD STATE: MA ZIP: 01824 FORMER COMPANY: FORMER CONFORMED NAME: BROOKS-PRI AUTOMATION INC DATE OF NAME CHANGE: 20020514 FORMER COMPANY: FORMER CONFORMED NAME: BROOKS AUTOMATION INC DATE OF NAME CHANGE: 19941215 10-Q 1 b73889bae10vq.htm BROOKS AUTOMATION, INC. FORM 10-Q e10vq

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, 2008


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 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 þ		Accelerated filer o		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 30, 2009:


Common stock, $0.01 par value		63,693,782 shares

BROOKS AUTOMATION, INC.

INDEX


	PAGE NUMBER
PART I. FINANCIAL INFORMATION
Item 1. Consolidated Financial Statements
Consolidated Balance Sheets as of December 31, 2008 (unaudited) and September 30, 2008		3
Consolidated Statements of Operations for the three months ended December 31, 2008 and 2007 (unaudited)		4
Consolidated Statements of Cash Flows for the three months ended December 31, 2008 and 2007 (unaudited)		5
Notes to Consolidated Financial Statements (unaudited)		6
Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations		15
Item 3. Quantitative and Qualitative Disclosure about Market Risk		20
Item 4. Controls and Procedures		20
PART II. OTHER INFORMATION
Item 1. Legal Proceedings		21
Item 2. Unregistered Sales of Equity Securities and Use of Proceeds		22
Item 6. Exhibits		22
Signatures		23
EX-10.01 AMENDED AND RESTATED 2000 EQUITY INCENTIVE PLAN, RESTATED AS OF DECEMBER 29, 2008
EX-31.01 Rule 13a-14(a), 15d-14(a) Certification
EX-31.02 Rule 13a-14(a), 15d-14(a) Certification
EX-32 Section 1350 Certification

BROOKS AUTOMATION, INC.

CONSOLIDATED BALANCE SHEETS

(unaudited)

(In thousands, except share and per share data)


	December 31,			September 30,
	2008			2008
Assets
Current assets
Cash and cash equivalents	$	78,100		$	110,269
Marketable securities		33,932			33,077
Accounts receivable, net		40,882			66,844
Insurance receivable for litigation		455			8,772
Inventories, net		109,559			105,901
Prepaid expenses and other current assets		14,368			13,783

Total current assets		277,296			338,646

Property, plant and equipment, net		82,931			81,604
Long-term marketable securities		47,625			33,935
Goodwill		119,938			119,979
Intangible assets, net		54,229			58,452
Equity investment in joint ventures		29,954			26,309
Other assets		3,292			4,713

Total assets	$	615,265		$	663,638


Liabilities, minority interests and stockholders’ equity
Current liabilities
Accounts payable	$	29,717		$	37,248
Deferred revenue		3,231			3,553
Accrued warranty and retrofit costs		7,938			8,174
Accrued compensation and benefits		17,014			18,174
Accrued restructuring costs		8,966			7,167
Accrued income taxes payable		2,884			3,151
Accrual for litigation settlement		—			7,750
Accrued expenses and other current liabilities		15,600			17,634

Total current liabilities		85,350			102,851
Accrued long-term restructuring		4,534			5,496
Income taxes payable		10,649			10,649
Other long-term liabilities		2,677			2,238

Total liabilities		103,210			121,234

Contingencies (Note 13)
Minority interests		322			409

Stockholders’ 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, 77,033,114 shares issued and 63,571,245 shares outstanding at December 31, 2008, 77,044,737 shares issued and 63,582,868 shares outstanding at September 30, 2008		770			770
Additional paid-in capital		1,790,371			1,788,891
Accumulated other comprehensive income		21,404			18,063
Treasury stock at cost, 13,461,869 shares at December 31, 2008 and September 30, 2008		(200,956	)		(200,956	)
Accumulated deficit		(1,099,856	)		(1,064,773	)

Total stockholders’ equity		511,733			541,995

Total liabilities, minority interests and stockholders’ equity	$	615,265		$	663,638

The accompanying notes are an integral part of these unaudited consolidated financial statements.

BROOKS AUTOMATION, INC.

CONSOLIDATED STATEMENTS OF OPERATIONS

(unaudited)

(In thousands, except per share data)


	Three months ended
	December 31,
	2008			2007
Revenues
Product	$	52,376		$	120,070
Services		21,067			27,763

Total revenues		73,443			147,833

Cost of revenues
Product		48,649			86,260
Services		18,406			23,124

Total cost of revenues		67,055			109,384

Gross profit		6,388			38,449

Operating expenses
Research and development		9,277			12,432
Selling, general and administrative		27,634			29,103
Restructuring and acquisition-related charges		4,105			600

Total operating expenses		41,016			42,135

Operating loss		(34,628	)		(3,686	)
Interest income		897			3,209
Interest expense		126			133
Loss on investment		1,185			—
Other (income) expense, net		38			343

Loss before income taxes, minority interests and equity in earnings of joint ventures		(35,080	)		(953	)
Income tax provision		391			670

Loss before minority interests and equity in earnings of joint ventures		(35,471	)		(1,623	)
Minority interests in income (loss) of consolidated subsidiaries		(87	)		(27	)
Equity in earnings of joint ventures		301			177

Net loss	$	(35,083	)	$	(1,419	)

Basic net loss per share	$	(0.56	)	$	(0.02	)

Diluted net loss per share	$	(0.56	)	$	(0.02	)

Shares used in computing loss per share
Basic		62,651			69,110
Diluted		62,651			69,110

The accompanying notes are an integral part of these unaudited consolidated financial statements.

BROOKS AUTOMATION, INC.

CONSOLIDATED STATEMENTS OF CASH FLOWS

(unaudited)

(In thousands)


	Three months ended
	December 31,
	2008			2007
Cash flows from operating activities
Net loss	$	(35,083	)	$	(1,419	)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization		8,380			8,507
Stock-based compensation		1,524			2,009
Amortization of discount on marketable securities		(34	)		(418	)
Undistributed earnings of joint ventures		(301	)		(177	)
Minority interests		(87	)		(27	)
(Gain) loss on disposal of long-lived assets		(8	)		105
Loss on investment		1,185			—
Changes in operating assets and liabilities, net of acquisitions and disposals:
Accounts receivable		26,330			14,379
Inventories		(3,252	)		(2,248	)
Prepaid expenses and other current assets		71			1,977
Accounts payable		(7,580	)		(14,396	)
Deferred revenue		(330	)		865
Accrued warranty and retrofit costs		(237	)		(1,413	)
Accrued compensation and benefits		(1,201	)		(6,362	)
Accrued restructuring costs		890			(1,691	)
Accrued expenses and other current liabilities		(3,745	)		(5,822	)

Net cash used in operating activities		(13,478	)		(6,131	)

Cash flows from investing activities
Purchases of property, plant and equipment		(5,084	)		(4,521	)
Purchases of marketable securities		(35,022	)		(98,115	)
Sale/maturity of marketable securities		22,533			114,154
Purchases of intangible assets		—			(75	)

Net cash provided by (used in) investing activities		(17,573	)		11,443

Cash flows from financing activities
Treasury stock purchases		—			(29,208	)

Net cash used in financing activities		—			(29,208	)

Effects of exchange rate changes on cash and cash equivalents		(1,118	)		223

Net decrease in cash and cash equivalents		(32,169	)		(23,673	)
Cash and cash equivalents, beginning of period		110,269			168,232

Cash and cash equivalents, end of period	$	78,100		$	144,559

The accompanying notes are an integral part of these unaudited consolidated financial statements.

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 for the year ended September 30, 2008. Certain reclassifications have been made in the prior period consolidated financial statements to conform to the current presentation.

Recently Enacted Accounting Pronouncements

In September 2006, the FASB issued SFAS No. 157, “Fair Value Measurements” (“SFAS 157”). SFAS 157 defines fair value, establishes a framework for measuring fair value in generally accepted accounting principles and expands disclosures about fair value measurements. In February 2008, the FASB issued FSP 157-1, “Application of FASB Statement No. 157 to FASB Statement No. 13 and Other Accounting Pronouncements That Address Fair Value Measurements for Purposes of Lease Classification or Measurement under Statement 13” (FSP 157-1) and FSP 157-2, “Effective Date of FASB Statement No. 157” (FSP 157-2). FSP 157-1 amends SFAS 157 to remove certain leasing transactions from its scope. As permitted by FSP 157-2, the effective date of SFAS 157 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), is the beginning of the Company’s first quarter of fiscal 2010. The measurement and disclosure requirements related to financial assets and financial liabilities are effective for the Company beginning on October 1, 2008. See Note 12.

In February 2007, the FASB issued SFAS No. 159, “The Fair Value Option for Financial Assets and Financial Liabilities — Including an Amendment of FASB Statement No. 115” (“SFAS 159”). SFAS 159 permits entities to choose to measure many financial instruments and certain other items at fair value and report unrealized gains and losses on items for which the fair value option has been elected in earnings at each subsequent reporting date. On October 1, 2008 the Company adopted SFAS 159 and has elected not to measure any additional financial instruments or other items at fair value.

In December 2007, the FASB issued SFAS No. 141 (revised 2007), “Business Combinations” (“SFAS 141R”). SFAS 141R 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. SFAS 141R applies prospectively to business combinations for which the acquisition date is on or after the beginning of the fiscal year beginning after December 15, 2008. SFAS 141R will be effective for the Company on October 1, 2009, and will be applied to any business combination with an acquisition date, as defined therein, that is subsequent to the effective date.

In December 2007, the FASB issued SFAS No. 160, “Noncontrolling Interests in Consolidated Financial Statements — An amendment of ARB No. 51” (“SFAS 160”). SFAS 160 amends ARB 51 to establish accounting and reporting standards for the noncontrolling interest in a subsidiary and for the deconsolidation of a subsidiary. It 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. SFAS 160 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 Statement requires that a parent recognize a gain or loss in net income when a subsidiary is deconsolidated. SFAS 160 is effective for fiscal years beginning after December 15, 2008. At this point in time, the Company believes that there will not be a material impact in connection with SFAS 160 on its financial position or results of operations.

In March 2008, the FASB issued SFAS No. 161, “Disclosures about Derivative Instruments and Hedging Activities — An amendment of FASB Statement No. 133” (“SFAS 161”). SFAS 161 amends and expands the disclosure requirements of SFAS 133 with the intent to provide users of financial statements with an enhanced understanding of (a) how and why an entity uses derivative instruments, (b) how derivative instruments and related hedged items are accounted for under SFAS 133 and its related interpretations, and (c) how derivative instruments and related hedged items affect an entity’s financial position, financial performance and cash flows. SFAS 161 is effective for fiscal years and interim periods beginning after November 15, 2008. The Company does not believe that the adoption of SFAS 161 will have a material impact on its financial position or results of operations.

In April 2008, the FASB issued FSP 142-3, “Determination of the Useful Life of Intangible Assets” (“FSP SFAS 142-3”). FSP SFAS 142-3 amends the factors that should be considered in developing renewal or extension assumptions used to determine the useful life of a recognized intangible asset under SFAS No. 142, “Goodwill and Other Intangible Assets” (“SFAS 142”). FSP SFAS 142-3 improves the consistency between the useful life of a recognized intangible asset under SFAS 142 and the period of expected cash flows used to measure the fair value of the asset under SFAS 141R and other applicable accounting literature. FSP SFAS 142-3 will be effective for the Company on October 1, 2009. The Company does not believe that the adoption of FSP SFAS 142-3 will have a material impact on its financial position or results of operations.

2. Stock Based Compensation

The following table reflects compensation expense recorded during the three months ended December 31, 2008 and 2007 in accordance with SFAS 123R (in thousands):


	Three months ended
	December 31,
	2008		2007
Stock options	$	133	$	189
Restricted stock		1,251		1,659
Employee stock purchase plan		140		161

	$	1,524	$	2,009

The Company uses the Black-Scholes valuation model for estimating the fair value of the stock options granted under SFAS No. 123R. 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. Restricted stock with market-based vesting criteria is valued using a lattice model.

Stock Option Activity

The following table summarizes stock option activity for the three months ended December 31, 2008:


				Weighted-
				Average	Weighted		Aggregate
	Number of			Remaining	Average		Intrinsic Value
	Options			Contractual Term	Exercise Price		(In Thousands)
Outstanding at September 30, 2008		1,816,025			$	19.92
Forfeited/expired		(158,852	)			24.89

Outstanding at December 31, 2008		1,657,173		1.9 years	$	19.44	$	3
Vested and unvested expected to vest at December 31, 2008		1,652,683		1.8 years	$	19.46	$	3
Options exercisable at December 31, 2008		1,577,687		1.8 years	$	19.75	$	3

The aggregate intrinsic value in the table above represents the total intrinsic value, based on the Company’s closing stock price of $5.81 as of December 31, 2008, 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, 2008 and 2007. The total intrinsic value of options exercised during the three month period ended December 31, 2008 and 2007 was $0. The total cash received from employees as a result of employee stock option exercises during the three months ended December 31, 2008 and 2007 was $0.

As of December 31, 2008 future compensation cost related to nonvested stock options is approximately $0.5 million and will be recognized over an estimated weighted average period of 1.4 years.

Restricted Stock Activity

A summary of the status of the Company’s restricted stock as of December 31, 2008 and changes during the three months ended December 31, 2008 is as follows:


	Three months ended
	December 31, 2008
				Weighted
				Average
				Grant-Date
	Shares			Fair Value
Outstanding at September 30, 2008		984,500		$	13.33
Awards vested		(31,999	)		12.84
Awards canceled		(5,751	)		17.04

Outstanding at December 31, 2008		946,750		$	13.33

The fair value of restricted stock awards vested during the three months ended December 31, 2008 and 2007 was $0.4 million and $1.8 million, respectively.

As of December 31, 2008, the unrecognized compensation cost related to nonvested restricted stock is $7.3 million and will be recognized over an estimated weighted average amortization period of 1.3 years.

Employee Stock Purchase Plan

There were no shares purchased under the employee stock purchase plan during the three months ended December 31, 2008.

Stock Repurchase Plan

On November 9, 2007 the Company announced that its Board of Directors authorized a stock repurchase plan to buy up to $200.0 million of the Company’s outstanding common stock. During the three months ended December 31, 2008, the Company purchased no shares of its common stock in connection with the stock repurchase plan.

3. Goodwill

The changes in the carrying amount of goodwill by reportable segment for the three months ended December 31, 2008 is as follows (in thousands):


						Global
	Automation		Critical			Customer
	Systems		Components			Operations			Total
Balance at September 30, 2008	$	—	$	55,741		$	64,238		$	119,979
Adjustments to goodwill:
Resolution of tax contingencies		—		(20	)		(21	)		(41	)

Balance at December 31, 2008	$	—	$	55,721		$	64,217		$	119,938

4. 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 state and international jurisdictions 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 2002. 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 $0.2 million will be realized in the fourth quarter of fiscal year 2009 as a result of the expiration of certain non-U.S. statute of limitations, all of which will impact the Company’s fiscal year 2009 effective tax rate.

On October 3, 2008, the Tax Extenders and Alternative Minimum Tax Relief Act of 2008 was enacted. This legislation retroactively reinstated the research and development tax credit, which had expired in 2007, for 2008. As the Company has a full valuation reserve, it will not recognize a benefit in the period ended December 31, 2008.

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,
	2008		2007
Weighted average common shares outstanding used in computing basic earnings (loss) per share		62,651		69,110
Dilutive common stock options and restricted stock awards		—		—

Weighted average common shares outstanding for purposes of computing diluted earnings (loss) per share		62,651		69,110

Approximately 1,670,000 and 2,367,000 options to purchase common stock and 875,000 and 555,000 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, 2008 and 2007, respectively, as their effect would be anti-dilutive. These options and restricted stock could, however, become dilutive in future periods.

6. Comprehensive Income (Loss)

The calculation of the Company’s comprehensive income (loss) for the three months ended December 31, 2008 and 2007 is as follows (in thousands):


	Three months ended
	December 31,
	2008			2007
Net loss	$	(35,083	)	$	(1,419	)
Change in cumulative translation adjustment		3,037			2,413
Unrealized gain (loss) on marketable securities		304			(832	)

	$	(31,742	)	$	162

7. Segment Information

The Company reports financial results in three segments: Automation Systems; Critical Components; and Global Customer Operations. In the second quarter of fiscal 2008 these segment disclosures were refined to reflect the results of a comprehensive review of operations conducted subsequent to the appointment of a new CEO and CFO. These refinements resulted in minor changes to the previously disclosed split of revenues and gross margins among segments and between products and services. A description of segments is included in the Company’s Annual Report on Form 10-K for the fiscal year ended September 30, 2008.

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. Amortization of acquired intangible assets (excluding completed technology) and restructuring 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 segment revenues. Segment assets exclude acquired intangible assets, goodwill, investments in joint ventures, marketable securities and cash equivalents.

Financial information for the Company’s business segments is as follows (in thousands):


							Global
	Automation			Critical			Customer
	Systems			Components			Operations			Total
Three months ended December 31, 2008
Revenues
Product	$	28,792		$	22,809		$	775		$	52,376
Services		—			—			21,067			21,067

	$	28,792		$	22,809		$	21,842		$	73,443

Gross profit (loss)	$	(3,421	)	$	6,961		$	2,848		$	6,388
Segment operating loss	$	(21,111	)	$	(3,951	)	$	(3,568	)	$	(28,630	)

Three months ended December 31, 2007
Revenues
Product	$	83,070		$	34,696		$	2,304		$	120,070
Services		—			—			27,763			27,763

	$	83,070		$	34,696		$	30,067		$	147,833

Gross profit	$	19,779		$	12,843		$	5,827		$	38,449
Segment operating income (loss)	$	(4,864	)	$	4,147		$	(684	)	$	(1,401	)

Assets
December 31, 2008	$	142,573		$	49,616		$	58,331		$	250,520
September 30, 2008	$	159,975		$	49,710		$	60,762		$	270,447

A reconciliation of the Company’s reportable segment operating income (loss) to the corresponding consolidated amounts for the three month periods ended December 31, 2008 and 2007 is as follows (in thousands):


	Three months ended
	December 31,
	2008			2007
Segment operating loss	$	(28,630	)	$	(1,401	)
Amortization of acquired intangible assets		1,893			1,685
Restructuring charges		4,105			600

Total operating loss	$	(34,628	)	$	(3,686	)

A reconciliation of the Company’s reportable segment assets to the corresponding consolidated amounts as of December 31, 2008 and September 30, 2008 is as follows (in thousands):


	December 31,		September 30,
	2008		2008
Segment assets	$	250,520	$	270,447
Goodwill		119,938		119,979
Intangible assets		54,229		58,452
Investments in cash equivalents, marketable securities and joint ventures		190,123		205,988
Insurance receivable		455		8,772

Total assets	$	615,265	$	663,638

8. Restructuring-Related Charges and Accruals

The Company recorded a charge to operations of $4,105,000 in the three months ended December 31, 2008 which primarily relates 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 three months ended December 31, 2008 were: Global Customer Operations — $2.7 million, Automated Systems — $0.8 million and Critical Components — $0.2 million. In addition, the Company incurred $0.4 million of restructuring charges for the three months ended December 31, 2008 that were related to general corporate functions that support all of the Company’s segments. The accruals for workforce reductions are expected to be paid over the next twelve months. The Company expects the annual salary and benefit savings as a result of these actions will be approximately $7.7 million. The cost savings resulting from these restructuring actions are expected to yield actual cash savings, net of the related costs, within twelve months.

The Company recorded a charge to operations of $600,000 in the three months ended December 31, 2007 which primarily relates to costs for workforce reductions of administrative personnel.

The activity for the three months ended December 31, 2008 and 2007 related to the Company’s restructuring-related accruals is summarized below (in thousands):


	Activity — Three Months Ended December 31, 2008
	Balance							Balance
	September 30,							December 31,
	2008		Expense		Utilization			2008
Facilities	$	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


	Activity — Three Months Ended December 31, 2007
	Balance							Balance
	September 30,							December 31,
	2007		Expense		Utilization			2007
Facilities	$	12,804	$	8	$	(905	)	$	11,907
Workforce-related		2,907		592		(1,364	)		2,135

	$	15,711	$	600	$	(2,269	)	$	14,042

The Company expects the majority of the remaining severance costs totaling $4,849,000 will be paid over the next twelve months. The expected facilities costs, totaling $8,651,000, net of estimated sub-rental income, will be paid on leases that expire through September 2011.

9. Gain (Loss) on Investment

During the three months ended December 31, 2008, the Company recorded a charge of $1.2 million to write-down its minority equity investment in a Swiss public company to its fair value as of the balance sheet date. This write-down reflects an other than temporary impairment of this investment. The remaining balance of this investment at December 31, 2008 after giving effect to foreign exchange was $0.4 million.

10. Other Balance Sheet Information

Components of other selected captions in the Consolidated Balance Sheets are as follows (in thousands):


	December 31,		September 30,
	2008		2008
Accounts receivable	$	42,379	$	68,210
Less allowances		1,497		1,366

	$	40,882	$	66,844

Inventories, net
Raw materials and purchased parts	$	65,835	$	64,651
Work-in-process		24,838		26,789
Finished goods		18,886		14,461

	$	109,559	$	105,901

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, 2008 and 2007 is as follows (in thousands):


Activity — Three Months Ended December 31, 2008
Balance						Balance
September 30,						December 31,
2008	Accruals		Settlements			2008
$8,174	$	1,873	$	(2,109	)	$	7,938


Activity — Three Months Ended December 31, 2007
Balance						Balance
September 30,						December 31,
2007	Accruals		Settlements			2007
$10,986	$	1,298	$	(2,715	)	$	9,569

11. 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, 2008 and 2007, the Company recorded income associated with UCI of $0.3 million and $0, respectively. At December 31, 2008, the carrying value of UCI in the Company’s consolidated balance sheet was $26.4 million. For the three months ended December 31, 2008 and 2007, royalty payments received by the Company from UCI were $0.2 million and $0, respectively.

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, 2008 and 2007, the Company recorded income associated with YBA of $0 and $0.2 million, respectively. At December 31, 2008, the carrying value of YBA in the Company’s consolidated balance sheet was $3.6 million. For the three months ended December 31, 2008 and 2007, revenues earned by the Company from YBA were $1.7 million and $3.8 million, respectively. The amount due from YBA included in accounts receivable at December 31, 2008 and September 30, 2008 was $4.9 million and $8.6 million, respectively. For the three months ended December 31, 2008 and 2007, the Company did not incur any charges from YBA for products or services. At December 31, 2008 and September 30, 2008 the Company owed YBA $0.2 million in connection with accounts payable for unpaid products and services.

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.

12. Fair Value Measurements

In September 2006, the FASB issued SFAS No. 157, “Fair Value Measurements,” (SFAS 157), which is effective for fiscal years beginning after November 15, 2007 and for interim periods within those years. This statement 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. SFAS 157 defines fair value based upon an exit price model.

Relative to SFAS 157, the FASB issued FASB Staff Positions (FSP) 157-1 and 157-2. FSP 157-1 amends SFAS 157 to exclude SFAS No. 13, “Accounting for Leases,” (SFAS 13) and its related interpretive accounting pronouncements that address leasing transactions, while FSP 157-2 delays the effective date of the application of SFAS 157 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.

The Company adopted SFAS 157 as of October 1, 2008, with the exception of the application of the statement to non-recurring non-financial assets and non-financial liabilities. Non-recurring non-financial assets and non-financial liabilities for which the Company has applied the provision of SFAS 157 include those measured at fair value in goodwill impairment testing, indefinite lived intangible assets measured at fair value for impairment testing, asset retirement obligations initially measured at fair value, and those initially measured at fair value in a business combination.

SFAS 157 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, 2008, 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	2008		(Level 1)		(Level 2)		(Level 3)
Assets
Cash Equivalents	$	23,408	$	23,408	$	—	$	—
Available-for-sale securities		81,389		16,781		64,608		—
Other Assets		415		415		—		—

Total Assets	$	105,212	$	40,604	$	64,608	$	—

Cash Equivalents

Cash equivalents of $23.4 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 $16.8 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 $64.6 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.

Other Assets

Other assets of $0.4 million, consisting of Stocks, are classified within Level 1 of the fair value hierarchy because they are valued using quoted market prices in active markets.

13. Contingencies

Regulatory Proceedings Relating to Equity Incentive Practices and the Restatement

All pending inquiries and investigations of the Company by agencies of the United States Government pertaining to the Company’s past equity incentive-related practices have now been concluded, as described more fully in the Company’s Annual Report on Form 10-K for the year ended September 30, 2008.

On July 25, 2007, a criminal indictment was filed in the United States District Court for the District of Massachusetts charging Robert J. Therrien, the former Chief Executive Officer and Chairman of the Company, with income tax evasion. Trial is scheduled to commence on March 9, 2009. A separate civil complaint was filed by the SEC on July 25, 2007 against Mr. Therrien in the United States District Court for the District of Massachusetts charging him with violations of federal securities laws. This matter has been stayed by the court pending the outcome of the criminal matter. In accordance with the provisions of the Company’s indemnification agreement with Mr. Therrien, the Company is advancing Mr. Therrien for costs he incurs in connection with these matters, which amounted to $1.8 million for the three months ended December 31, 2008.

Private Litigation

All private class action and derivative action matters commenced against the Company relating to past equity incentive-related practices have been concluded or dismissed, as described more fully in the Company’s Annual Report on Form 10-K for the year ended September 30, 2008.

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 the Company, from Mr. Therrien 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 referenced above, 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. Brooks is a nominal defendant in the consolidated action and any recovery in this action, less attorneys’ fees, would go to the Company. 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.

Matter to which the Company is Not a Party

Jenoptik-Asyst Litigation

The Company acquired certain assets, including a transport system known as IridNet, from the Infab division of Jenoptik AG on September 30, 1999. Asyst Technologies, Inc. had previously filed suit against Jenoptik AG and other defendants, or collectively, the defendants, in the Northern District of California charging that products of the defendants, including IridNet, infringe Asyst’s U.S. Patent Nos. 4,974,166, or the ’166 patent, and 5,097,421, or the ’421 patent. Asyst later withdrew its claims related to the ’166 patent from the case. Summary judgment of noninfringement was granted in that case by the District Court and judgment was issued in favor of Jenoptik on the ground that the product at issue did not infringe the asserted claims of the ’421 patent. Following certain rulings and findings adverse to Jenoptik, on August 3, 2007 the District Court issued final judgment in favor of Jenoptik. Asyst appealed, and on October 10, 2008, the United States Court of Appeals for the Federal Circuit entered an order affirming the District Court’s final judgment in favor of Jenoptik.

The Company had received notice that Asyst might amend its complaint in this Jenoptik litigation to name Brooks as an additional defendant, but no such action was ever taken. Based on the Company’s investigation of Asyst’s allegations, the Company does not believe it is infringing any claims of Asyst’s patents. Asyst may decide to seek to prohibit the Company from developing, marketing and using the IridNet product without a license. The Company cannot guarantee that a license would be available to Brooks on reasonable terms, if at all. In any case, the Company could face litigation with Asyst. Jenoptik has agreed to indemnify the Company for any loss Brooks may incur in this action.

Litigation is inherently unpredictable and the Company cannot predict the outcome of the legal proceedings described above with any certainty. Should there be an adverse judgment against the Company, it may have a material adverse impact on its financial statements. Because of uncertainties related to both the amount and range of losses in the event of an unfavorable outcome in the lawsuits listed above or in certain other pending proceedings for which loss estimates have not been recorded, the Company is unable to make a reasonable estimate of the losses that could result from these matters and hence has recorded no accrual in its financial statements as of December 31, 2008.

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 77% of our consolidated revenues for fiscal year 2008. We also provide unique solutions to customers in data storage, advanced display, analytical instruments and solar 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 2006 and throughout most of fiscal 2007, we benefited from an industry expansion. During the fourth quarter of fiscal 2007, we began to observe a slowdown in the demand for semiconductor capital equipment. This slowdown continued throughout fiscal year 2008. In response to this slowdown, we reduced our workforce by approximately 15% during fiscal year 2008.

Demand for our products has continued to decrease in fiscal year 2009 as a result of the global economic slowdown. In response to these further weaknesses in demand, we are developing plans to further reduce our cost structure, including further reductions to the size of our workforce. We reduced our workforce by approximately 10% during the first quarter of fiscal 2009, and we plan to further reduce our workforce by approximately 20%, with most of those reductions occurring during the second quarter of fiscal 2009. We have not completed the assessment of our cost structure, which may result in further workforce reductions.

Our current internal reporting structure includes three segments: Automation Systems, Critical Components and Global Customer Operations. Our restructuring actions will likely change our internal reporting structure. We will continue to report our financial results for our existing segments until our internal reporting structure changes are complete. We expect the changes to our internal reporting structure to be complete during fiscal 2009.

As a result of our acquisitions, we have identified intangible assets and generated significant goodwill. Intangible assets are valued based on estimates of future cash flows and amortized over their estimated useful life. Goodwill is subject to annual impairment testing as well as testing upon the occurrence of any event that indicates a potential impairment. Intangible assets and other long-lived assets are subject to an impairment test if there is an indicator of impairment. We have $174.2 million of intangible assets on our unaudited consolidated balance sheet as of December 31, 2008, including $119.9 million of goodwill. As of December 31, 2008, two of our three reportable segments have goodwill balances. The changes we will make to our internal reporting structure and to how we operate our business will likely result in the re-allocation of our goodwill to our newly identified reporting units based on factors such as the relative fair values of these reporting units. To the extent goodwill allocated to each new reporting unit causes the carrying value of any reporting unit to exceed its fair value, we may record an impairment charge which could be material.

As of December 31, 2008, we had total inventory of $109.6 million including $70.2 of inventory related to our Automation Systems segment, $15.7 million of inventory related to our Critical Components segment and $23.7 million of inventory for our Global Customer Operations segment. During the three months ended December 31, 2008, we recorded aggregate charges for excess and obsolete inventory of $3.9 million which primarily relates to our Automation Systems segment, and was the result of decreased demand for semiconductor capital equipment. If the weakness in the semiconductor capital equipment market continues for an extended period of time, we may be required to record additional material provisions for excess and obsolete inventory which will decrease our gross margin in the period we record these charges.

We have provided allowances on our accounts receivable of $1.5 million as of December 31, 2008, which we believe is appropriate based on our assessment of our higher risk accounts. Should the current weakness in the semiconductor market continue for an extended period of time, more of our customers may be adversely impacted and we may be required to record additional material provisions for bad debts.

Three Months Ended December 31, 2008, Compared to Three Months Ended December 31, 2007

Revenues

We reported revenues of $73.4 million for the three months ended December 31, 2008, compared to $147.8 million in the same prior year period, a 50.3% decrease. The total decrease in revenues of $74.4 million impacted our segments as follows: Automation Systems segment revenues decreased by $54.3 million, Critical Components segment revenues decreased by $11.9 million and our Global Customer Operations segment revenues decreased by $8.2 million. These decreases were the result of lower volume shipments in response to declining demand. We expect the volume of shipments to further decline in the near term in response to the global economic slowdown.

Our Automation Systems segment reported revenues of $28.8 million for the three months ended December 31, 2008, compared to $83.1 million in the same prior year period, a 65.3% decrease. This decrease is attributable to weaker demand for semiconductor capital equipment and impacted all product lines within this segment.

Our Critical Components segment reported revenues of $22.8 million for the three months ended December 31, 2008, compared to $34.7 million, a 34.3% decrease. This decrease principally reflects lower revenues of $10.4 million for cryogenic vacuum pumping, primarily due to the decrease in demand for semiconductor capital equipment. Revenues from non-semiconductor related customers were approximately 62% of our Critical Components revenues for the three months ended December 31, 2008 as compared to 48% in the same prior year period.

Global Customer Operations segment reported revenues of $21.8 million for the three months ended December 31, 2008, compared to $30.1 million in the same prior year period, a 27.6% decrease. This decrease is attributable to lower service contract and repair revenue of $6.7 million and lower legacy product revenue of $1.6 million. Our consolidated service revenues are all earned by our Global Customer Operations segment, and include the revenues from the sale of spare parts. Service revenues for the three months ended December 31, 2008 were $21.1 million as compared to $27.8 million for the same prior year period, a decrease of 24.1%. This decrease is primarily the result of decreased spending by semiconductor manufacturing and semiconductor capital equipment companies.

Gross Profit

Gross margin dollars decreased to $6.4 million for the three months ended December 31, 2008 as compared to $38.4 million for the same prior year period. This decrease is primarily the result of the $74.4 million in lower revenue. Gross margin percentage decreased to 8.7% for the three months ended December 31, 2008 as compared to 26.0% for the same prior year period. The decrease in gross margin percentage is primarily due to the lower absorption of indirect factory overhead on lower revenues.

Gross margin dollars from our Automation Systems segment decreased to a loss of $3.4 million for the three months ended December 31, 2008 as compared to income of $19.8 million for the same prior year period. This decrease is due to a drop of $54.3 million in revenues, and a $2.0 million increase in charges for excess and obsolete inventory. Gross margin percentage decreased to (11.9)% for the three months ended December 31, 2008 as compared to 23.8% in the same prior year period. The decrease is due to increased charges for excess and obsolete inventory which lowered gross margin by 6.9%, with the balance of the decrease related primarily to lower absorption of indirect factory overhead on lower revenues.

Gross margin dollars from our Critical Components segment decreased to $7.0 million for the three months ended December 31, 2008 as compared to $12.8 million for the same prior year period. The decrease is primarily related to an $11.9 million decrease in revenues. Gross margin percentage was 30.7% for the three months ended December 31, 2008 as compared to 36.9% in the same prior year period. The decrease in gross margin percentage is primarily due to the lower absorption of indirect factory overhead on lower revenues.

Gross margin dollars from our Global Customer Operations segment decreased to $2.8 million for the three months ended December 31, 2008 as compared to $5.8 million for the same prior year period. This decrease is the result of lower service revenues of $6.7 million and lower legacy product revenues of $1.6 million. Gross margin percentage was 12.8% for the three months ended December 31, 2008 as compared to 19.3% for the same prior year period. This decrease is due to higher revenues from highly profitable legacy product sales in the prior year period which impacted gross profit percentage by 3.4%, with the balance of the decrease attributable to lower absorption of service costs on less revenue.

Research and Development

Research and development, or R&D, expenses for the three months ended December 31, 2008 were $9.3 million as compared to $12.4 million for the same prior year period. This decrease includes reduced labor costs of $1.9 million and reductions in third party material and service costs of $0.6 million. These decreases are primarily associated with reduced Automation Systems product development with certain development cycles coming to completion.

Selling, General and Administrative

Selling, general and administrative expenses were $27.6 million for the three months ended December 31, 2008 as compared to $29.1 million for the same prior year period. This decrease includes lower cash-based labor costs of $2.5 million and lower stock-based compensation costs of $0.4 million. These decreases were partially offset by a $0.7 million increase in litigation costs incurred by us to indemnify a former executive. We settled our litigation matters with the SEC during fiscal 2008, however, we continue to incur litigation costs relating to our former executive officer that we are contractually required to indemnify. The total indemnification costs were $1.8 million for the three months ended December 31, 2008.

Restructuring Charges

We recorded a charge of $4.1 million for the three months ended December 31, 2008 as an initial charge for our fiscal 2009 restructuring plan. This charge consists primarily of $4.1 million 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 three months ended December 31, 2008 were: Global Customer Operations — $2.7 million, Automated Systems — $0.8 million and Critical Components - - $0.2 million. In addition, we incurred $0.4 million of restructuring charges for the three months ended December 31, 2008 that were related to general corporate functions that support all of our segments. The accruals for workforce reductions are expected to be paid over the next twelve months. We expect the annual salary and benefit savings as a result of these actions will be approximately $7.7 million. The cost savings resulting from these restructuring actions are expected to yield actual cash savings, net of the related costs, within twelve months. We have not completed all actions under our fiscal 2009 restructuring plan, and expect to make further workforce reductions during fiscal 2009. We expect to incur severance charges of approximately $6.0 million to $8.0 million, primarily in our second quarter of fiscal 2009, in connection with planned workforce reductions of an additional 300 employees. We are continuing to review the costs of our operations, and may make further reductions in our workforce resulting in additional severance costs.

We recorded a restructuring charge of $0.6 million for the three months ended December 31, 2007 which primarily relates to costs for workforce reductions of administrative personnel.

Interest Income and Expense

Interest income decreased by $2.3 million, to $0.9 million, for the three months ended December 31, 2008. Approximately $1.2 million of this decrease is attributable to lower interest rates on our investments, with the balance due to lower investment balances.

Gain (Loss) on Investment

During the three months ended December 31, 2008, we recorded a charge of $1.2 million to write down our minority equity investment in a closely-held Swiss public company. The remaining balance of this investment at December 31, 2008 after giving effect to foreign exchange was $0.4 million.

Income Tax Provision

We recorded an income tax provision of $0.4 million for the three months ended December 31, 2008, which is principally attributable to taxes on foreign income and interest related to unrecognized tax benefits. We recorded an income tax provision of $0.7 million for the three months ended December 31, 2007, which is principally attributable to alternative minimum taxes along with 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, 2008, 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.

Equity in Earnings of Joint Ventures

Income associated with our 50% interest in ULVAC Cryogenics, Inc., a joint venture with ULVAC Corporation of Japan, was $0.3 million for the three months ended December 31, 2008, compared to $0 for the same prior year period. Income associated with our 50% interest in Yaskawa Brooks Automation, Inc., a joint venture with Yaskawa Electric Corporation of Japan was $0 for the three months ended December 31, 2008 as compared to $0.2 million for the same prior year period.

The carrying values of our joint venture investments included in our consolidated balance sheet at December 31, 2008 were $30.0 million, including $26.4 million for our ULVAC joint venture and $3.6 million for our Yaskawa joint venture.

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. In response to these downturns, we have and are continuing to implement cost reduction programs aimed at aligning our ongoing operating costs with our currently expected revenues over the near term. These cost management initiatives include consolidating facilities, reductions to headcount and reduced spending. The cyclical nature of the industry make estimates of future revenues, results of operations and net cash flows inherently uncertain.

At December 31, 2008, we had cash, cash equivalents and marketable securities aggregating $159.6 million. This amount was comprised of $78.1 million of cash and cash equivalents, $33.9 million of investments in short-term marketable securities and $47.6 million of investments in long-term marketable securities.

Cash and cash equivalents were $78.1 million at December 31, 2008, a decrease of $32.2 million from September 30, 2008. This decrease was primarily due to $13.5 million of cash used by operating activities, capital expenditures of $5.1 million and $12.5 million of net purchases of marketable securities.

Cash used in operations was $13.5 million for the three months ended December 31, 2008, and was primarily attributable to a $24.1 million loss after adjusting our net loss for non-cash expenses, including depreciation and amortization of $8.4 million, stock-based compensation of $1.5 million, and other non-cash items of $0.7 million. Cash used in operations was partially offset by $10.9 million of changes in working capital which was primarily due to decreased accounts receivable balances of $26.3 million which was partially offset by lower accounts payable levels of $7.6 million, lower accrued expenses of $4.3 million and increased inventory of $3.3 million. The increases in inventory relate primarily to our Global Customer Operations segment to improve customer responsiveness.

Cash used in investing activities was $17.6 million for the three months ended December 31, 2008, and is principally comprised of net purchases of marketable securities of $12.5 million and $5.1 million of capital expenditures, including $3.0 million in expenditures related to our Oracle ERP implementation. Our Oracle ERP implementation is expected to cost approximately $26.5 million when fully implemented, of which $23.7 million has been incurred from inception through December 31, 2008.

At December 31, 2008, we had approximately $0.5 million of letters of credit outstanding.

On November 9, 2007 we announced that our Board of Directors authorized a stock repurchase plan to buy up to $200.0 million of our outstanding common stock. During the year ended September 30, 2008, we purchased 7,401,869 shares of our common stock for a total of $90.2 million in connection with the stock repurchase plan. We did not repurchase any of our stock during the three months ended December 31, 2008. Management and the Board of Directors will exercise discretion with respect to the timing and amount of any future shares repurchased, if any, based on their evaluation of a variety of factors, including current market conditions. Repurchases may be commenced or suspended at any time without prior notice. The repurchase program has been funded using our available cash resources. Any future repurchases would come from our available cash resources.

We believe that we have adequate resources to fund our currently planned working capital and capital expenditure requirements for both the short and long-term. However, the cyclical nature of the semiconductor industry and the current global economic downturn 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. In addition, we are subject to indemnification obligations in connection with our stock-based compensation restatement with certain former executives which could have an adverse affect on our existing resources.

Recently Enacted Accounting Pronouncements

In September 2006, the FASB issued SFAS No. 157, “Fair Value Measurements” (“SFAS 157”). SFAS 157 defines fair value, establishes a framework for measuring fair value in generally accepted accounting principles and expands disclosures about fair value measurements. In February 2008, the FASB issued FSP 157-1, “Application of FASB Statement No. 157 to FASB Statement No. 13 and Other Accounting Pronouncements That Address Fair Value Measurements for Purposes of Lease Classification or Measurement under Statement 13” (FSP 157-1) and FSP 157-2, “Effective Date of FASB Statement No. 157” (FSP 157-2). FSP 157-1 amends SFAS 157 to remove certain leasing transactions from its scope. As permitted by FSP 157-2, the effective date of SFAS 157 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), is the beginning of our first quarter of fiscal 2010. The measurement and disclosure requirements related to financial assets and financial liabilities are effective for us beginning on October 1, 2008. See Note 12.

In February 2007, the FASB issued SFAS No. 159, “The Fair Value Option for Financial Assets and Financial Liabilities — Including an Amendment of FASB Statement No. 115” (“SFAS 159”). SFAS 159 permits entities to choose to measure many financial instruments and certain other items at fair value and report unrealized gains and losses on items for which the fair value option has been elected in earnings at each subsequent reporting date. On October 1, 2008 we adopted SFAS 159 and have elected not to measure any additional financial instruments or other items at fair value.

In December 2007, the FASB issued SFAS No. 160, “Noncontrolling Interests in Consolidated Financial Statements — An amendment of ARB No. 51” (“SFAS 160”). SFAS 160 amends ARB 51 to establish accounting and reporting standards for the noncontrolling interest in a subsidiary and for the deconsolidation of a subsidiary. It 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. SFAS 160 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 Statement requires that a parent recognize a gain or loss in net income when a subsidiary is deconsolidated. SFAS 160 is effective for fiscal years beginning after December 15, 2008. At this point in time, we believe that there will not be a material impact in connection with SFAS 160 on our financial position or results of operations.

In March 2008, the FASB issued SFAS No. 161, “Disclosures about Derivative Instruments and Hedging Activities — An amendment of FASB Statement No. 133” (“SFAS 161”). SFAS 161 amends and expands the disclosure requirements of SFAS 133 with the intent to provide users of financial statements with an enhanced understanding of (a) how and why an entity uses derivative instruments, (b) how derivative instruments and related hedged items are accounted for under SFAS 133 and its related interpretations, and (c) how derivative instruments and related hedged items affect an entity’s financial position, financial performance and cash flows. SFAS 161 is effective for fiscal years and interim periods beginning after November 15, 2008. We do not believe that the adoption of SFAS 161 will have a material impact on our financial position or results of operations.

In April 2008, the FASB issued FSP 142-3, “Determination of the Useful Life of Intangible Assets” (“FSP SFAS 142-3”). FSP SFAS 142-3 amends the factors that should be considered in developing renewal or extension assumptions used to determine the useful life of a recognized intangible asset under SFAS No. 142, “Goodwill and Other Intangible Assets” (“SFAS 142”). FSP SFAS 142-3 improves the consistency between the useful life of a recognized intangible asset under SFAS 142 and the period of expected cash flows used to measure the fair value of the asset under SFAS 141R and other applicable accounting literature. FSP SFAS 142-3 will be effective for us on October 1, 2009. We do not believe that the adoption of FSP SFAS 142-3 will have a material impact on our financial position or 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, 2008, the unrealized gain on marketable securities, excluding our investment in a Swiss public company, was $304,000. A hypothetical 100 basis point change in interest rates would result in an annual change of approximately $1.7 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 22.0% of our total sales for the three months ended December 31, 2008. We also purchase materials from some suppliers outside of the United States that is transacted in currencies other than the U.S. dollar. In the three months ended December 31, 2008, we recorded foreign exchange losses related to receivables of $0.1 million, and no foreign exchange losses related to payables. If currency exchange rates had been 10% different throughout the three months ended December 31, 2008 compared to the currency exchange rates actually experienced, the impact on our net earnings would have been approximately $0.5 million. The changes in currency exchange rates relative to the U.S. dollar during the three months ended December 31, 2008 compared to the currency exchange rates at September 30, 2008 resulted in an increase in net assets of $3.0 million that we reported as a separate component of comprehensive income. The impact of a hypothetical 10% change in foreign exchange rates at December 31, 2008 is not considered material.

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, our chief executive officer and chief financial officer have concluded that our disclosure controls and procedures are effective to ensure that information required to be disclosed by us in the reports that we file under the Securities Exchange Act of 1934 is recorded, processed, summarized and reported in accordance with the time specified by the SEC’s rules and forms.

Change in Internal Controls. There were no changes in our internal control over financial reporting that occurred during our last fiscal quarter that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

PART II. OTHER INFORMATION

Item 1. Legal Proceedings

Regulatory Proceedings Relating to Equity Incentive Practices and the Restatement

All pending inquiries and investigations of the Company by agencies of the United States Government pertaining to our past equity incentive-related practices have now been concluded, as described more fully in our Annual Report on Form 10-K for the year ended September 30, 2008.

On July 25, 2007, a criminal indictment was filed in the United States District Court for the District of Massachusetts charging Robert J. Therrien, the former Chief Executive Officer and Chairman of the Company, with income tax evasion. Trial is scheduled to commence on March 9, 2009. A separate civil complaint was filed by the SEC on July 25, 2007 against Mr. Therrien in the United States District Court for the District of Massachusetts charging him with violations of federal securities laws. This matter has been stayed by the court pending the outcome of the criminal matter. In accordance with the provisions of the Company’s indemnification agreement with Mr. Therrien, we are advancing Mr. Therrien for costs he incurs in connection with these matters, which amounted to $1.8 million for the three months ended December 31, 2008.

Private Litigation

All private class action and derivative action matters commenced against the Company relating to past equity incentive-related practices have been concluded or dismissed, as described more fully in our Annual Report on Form 10-K for the year ended September 30, 2008.

Matter to which the Company is Not a Party

Jenoptik-Asyst Litigation

We acquired certain assets, including a transport system known as IridNet, from the Infab division of Jenoptik AG on September 30, 1999. Asyst Technologies, Inc. had previously filed suit against Jenoptik AG and other defendants, or collectively, the defendants, in the Northern District of California charging that products of the defendants, including IridNet, infringe Asyst’s U.S. Patent Nos. 4,974,166, or the ’166 patent, and 5,097,421, or the ’421 patent. Asyst later withdrew its claims related to the ’166 patent from the case. Summary judgment of noninfringement was granted in that case by the District Court and judgment was issued in favor of Jenoptik on the ground that the product at issue did not infringe the asserted claims of the ’421 patent. Following certain rulings and findings adverse to Jenoptik, on August 3, 2007 the District Court issued final judgment in favor of Jenoptik. Asyst appealed, and on October 10, 2008, the United States Court of Appeals for the Federal Circuit entered an order affirming the District Court’s final judgment in favor of Jenoptik.

We had received notice that Asyst might amend its complaint in this Jenoptik litigation to name Brooks as an additional defendant, but no such action was ever taken. Based on our investigation of Asyst’s allegations, we do not believe it is infringing any claims of Asyst’s patents. Asyst may decide to seek to prohibit us from developing, marketing and using the IridNet product without a license. We cannot guarantee that a license would be available to us on reasonable terms, if at all. In any case, we could face litigation with Asyst. Jenoptik has agreed to indemnify us for any loss we may incur in this action.

Litigation is inherently unpredictable and we cannot predict the outcome of the legal proceedings described above with any certainty. Should there be an adverse judgment against us, it may have a material adverse impact on our financial statements. Because of uncertainties related to both the amount and range of losses in the event of an unfavorable outcome in the lawsuits listed above or in certain other pending proceedings for which loss estimates have not been recorded, we are unable to make a reasonable estimate of the losses that could result from these matters and hence have recorded no accrual in our financial statements as of December 31, 2008.

Item 2. Unregistered Sales of Equity Securities and Use of Proceeds

On November 9, 2007, we announced that our Board of Directors authorized a stock repurchase plan to buy up to $200.0 million of our outstanding common stock. We did not repurchase any of our stock under this program during the three months ended December 31, 2008.

The following table provides information concerning shares of the Company’s 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, 2008. 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, 2008		1,584	$	6.46		1,584	$	—
November 1 — 30, 2008		6,038		5.67		6,038		—
December 1 — 31, 2008		—		—		—		—


Total		7,622	$	5.83		7,622	$	—

Item 6. Exhibits

The following exhibits are included herein:


Exhibit No.		Description
10.01		Amended and Restated 2000 Equity Incentive Plan, Restated as of December 29, 2008

31.01		Rule 13a-14(a), 15d-14(a) Certification

31.02		Rule 13a-14(a), 15d-14(a) Certification

32		Section 1350 Certifications

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 9, 2009	/s/ Martin S. Headley
	Martin S. Headley
	Executive Vice President and Chief Financial Officer (Principal Financial Officer)


DATE: February 9, 2009	/s/ Timothy S. Mathews
	Timothy S. Mathews
	Vice President and Corporate Controller (Principal Accounting Officer)

EXHIBIT INDEX


Exhibit No.		Description
10.01		Amended and Restated 2000 Equity Incentive Plan, Restated as of December 29, 2008

31.01		Rule 13a-14(a), 15d-14(a) Certification

31.02		Rule 13a-14(a), 15d-14(a) Certification

32		Section 1350 Certifications

EX-10.01 2 b73889baexv10w01.htm EX-10.01 AMENDED AND RESTATED 2000 EQUITY INCENTIVE PLAN, RESTATED AS OF DECEMBER 29, 2008 exv10w01

Exhibit 10.01

BROOKS AUTOMATION, INC.

AMENDED AND RESTATED 2000 EQUITY INCENTIVE PLAN
(formerly known as the 2000 Combination Stock Option Plan)
Restated as of December 29, 2008

Section 1. Purpose

The purpose of the Brooks Automation, Inc. Amended and Restated 2000 Equity Incentive Plan (the “Plan”) is to attract and retain key employees, independent directors, consultants and advisors. The Plan provides an incentive for these Participants to assist Brooks Automation, Inc. (the “Company”) to achieve long-range performance goals, and to enable them to participate in the long-term growth of the Company.

Section 2. Definitions

(a)		“Affiliate” means any corporation or other entity that stands in a relationship to the Company that would result in the Company and such corporation or other entity being treated as one employer under Section 414(b) or Section 414(c) of the Code, except that in determining eligibility for the grant of a Stock Option or SAR by reason of service for an Affiliate, Sections 414(b) and 414(c) of the Code shall be applied by substituting “at least 50%” for “at least 80%” under Section 1563(a)(1), (2) and (3) of the Code and Treas. Regs. § 1.414(c)-2; provided, that to the extent permitted under Section 409A, “at least 20%” shall be used in lieu of “at least 50%”; and further provided, that the lower ownership threshold described in this definition (50% or 20% as the case may be) shall apply only if the same definition of affiliation is used consistently with respect to all compensatory stock options or stock awards (whether under the Plan or another plan). The Company may at any time by amendment provide that different ownership thresholds (consistent with Section 409A of the Code) apply. Notwithstanding the foregoing provisions of this definition, except as otherwise determined by the Committee a corporation or other entity shall be treated as an Affiliate only if its employees would be treated as employees of the Company for purposes of the rules promulgated under the Securities Act of 1933, as amended, with respect to the use of Form S-8.

(b)		“Award” means any Option, Stock Appreciation Right, Performance or Award Share, or Restricted Stock awarded under the Plan.

(c)		“Board” means the Board of Directors of the Company.

(d)		“Code” means the Internal Revenue Code of 1986, as amended from time to time.

(e)		“Committee” means the Compensation Committee of the Board, or such other Committee of not less than two independent members of the Board appointed by the Board to administer the Plan. If at any time the Compensation Committee consists of members, one or more of whom do not qualify as independent, non-employee or outside directors (for purposes of applicable stock exchange rules, the requirements of Rule 16b-3 promulgated under the Exchange Act, and the requirements of Section 162(m) of the Code), it shall act in respect of the Plan through a subcommittee of two or more members, all of whom so qualify, and all references herein to the Committee shall be deemed to refer to such subcommittee.

(f)		“Common Stock” or “Stock” means the Common Stock, par value $.01 per share, of the Company.

(g)		“Company” means Brooks Automation, Inc.

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(h)		“Covered Transaction” means any of (i) a consolidation, merger, or similar transaction or series of related transactions, including a sale or other disposition of stock, in which the Company is not the surviving corporation or which results in the acquisition of all or substantially all of the Company’s then outstanding common stock by a single person or entity or by a group of persons and/or entities acting in concert, (ii) a sale or transfer of all or substantially all the Company’s assets, or (iii) a dissolution or liquidation of the Company. Where a Covered Transaction involves a tender offer that is reasonably expected to be followed by a merger described in clause (i) (as determined by the Committee), the Covered Transaction shall be deemed to have occurred upon consummation of the tender offer.

(i)		“Designated Beneficiary” means the beneficiary designated by a Participant, in a manner determined by the Committee, to receive amounts due or exercise rights of the Participant in the event of the Participant’s death. In the absence of an effective designation by a Participant, Designated Beneficiary shall mean the Participant’s estate.

(j)		“Exchange Act” means the Securities Exchange Act of 1934, as amended from time to time, or any successor statue.

(k)		“Fair Market Value” means, (i) the closing sales price, if any, on a national securities exchange or automated quotation system on the date as of which Fair Market Value is being determined or, if none, shall be the closing sales price on the nearest trading date before that date; and (ii) if the Common Stock is then traded on an exchange or system which does not have sale price reporting, the mean between the average of the “Bid” and the average of the “Ask” prices, if any, as reported for the date as of which Fair Market Value is being determined. Fair Market Value shall be determined in a manner consistent with the requirements under Section 409A of the Code.

(l)		“Incentive Stock Option” means an option to purchase shares of Common Stock awarded to a Participant under Section 6 which is intended to meet the requirements of Section 422 of the Code or any successor provision.

(m)		“Non-Qualified Stock Option” means an option to purchase shares of Common Stock, awarded to a Participant under Section 6, which does not meet the requirements of Section 422 of the Code or any successor provision. Each option granted under the Plan shall be deemed to be, by its terms, a Non-Qualified Stock Option unless it is expressly designated as an Incentive Stock Option.

(n)		“Option” means a Nonqualified Stock Option or Incentive Stock Option.

(o)		“Participant” means a person eligible pursuant to Section 3 hereof and selected by the Committee to receive an Award under the Plan.

(p)		“Performance Cycle” or “Cycle” means the period of time selected by the Committee during which performance is measured for the purpose of determining the extent to which a Performance Award has been earned.

(q)		“Performance Award” means an Award awarded to a Participant under Section 8 that is subject to one or more specified performance conditions, other than the mere passage of time, the satisfaction of which is a condition for the grant, exercisability, vesting or full enjoyment of an Award. The term “specified performance condition” means, in the case of Performance Awards

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other than Options or SARs, an objectively determinable measure of performance relating to any or any combination of the following (measured either absolutely or by reference to an index or indices and determined either on a combined basis or, as the context permits, on a divisional, subsidiary, line of business, project or geographical basis or in combinations thereof): sales; revenues; assets; expenses; earnings before or after deduction for all or any portion of interest, taxes, depreciation or amortization, whether or not on a continuing operations or an aggregate or per share basis; return on equity, investment, capital or assets; one or more operating ratios; borrowing levels, leverage ratios or credit rating; market share; capital expenditures; cash flow; stock price; stockholder return; sales of particular products or services; customer acquisition or retention; acquisitions and divestitures (in whole or in part); joint ventures and strategic alliances; spin-offs, split-ups and the like; reorganizations; or recapitalizations, restructurings, financings (issuances of debt or equity) or refinancings. Such criteria and any targets with respect thereto determined by the Committee need not be based on an increase, a positive or improved result or avoidance of loss. To the extent consistent with the requirements for satisfying the performance-based compensation exception under Section 162(m), the Committee may provide in the case of any Award intended to qualify for such exception that one or more of the criteria applicable to such Award will be adjusted in an objectively determinable manner to reflect events (for example, but without limitation, acquisitions or dispositions) occurring during the performance period that affect the applicable criteria.

(r)		“Permanent Disability” has the meaning specified in Section 22(e)(3) of the Code.

(s)		“Restricted Period” means the period of time selected by the Committee during which a share of Restricted Stock may be forfeited to the Company.

(t)		“Restricted Stock” means shares of Common Stock subject to forfeiture, awarded to a Participant under Section 9.

(u)		“Stock Appreciation Right” or “SAR” means a right to receive any excess in value of shares of Common Stock over the exercise price, awarded to a Participant under Section 7.

(v)		“Stock Unit” means an award of Common Stock and/or other rights granted as units that are valued in whole or in part by reference to, or otherwise based on, the value of Common Stock, awarded to a Participant under Section 10.

Section 3. Eligibility

All key employees, independent directors, consultants and advisors of the Company or any Affiliate capable of contributing significantly to the successful performance of the Company, other than a person who has irrevocably elected not to be eligible, are eligible to be selected by the Committee to be Participants in the Plan.

Section 4. Stock Available for Awards

(a)

Subject to adjustment under subsection (b), Awards may be made under the Plan to acquire not in excess of 9,000,000 shares of Company Common Stock. Subject to adjustment under subsection (b), the maximum aggregate number of shares of the Company’s Common Stock for which option grants may be made to any person during any fiscal year shall be 500,000 shares and the maximum aggregate number of shares of the Company’s Common Stock for which

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		other awards may be made to any one person during any fiscal year shall be 250,000 shares; provided, however, that up to an additional 100,000 shares of Common Stock may be granted as other awards during any fiscal year to the Chief Executive Officer of the Company as an inducement to become employed (or reemployed) by the Company. If any Award in respect of shares of Common Stock expires or is terminated unexercised or is forfeited for any reason or settled in a manner that results in fewer shares outstanding than were initially awarded, including without limitation the surrender of shares in payment for the Award or any tax obligation thereon, the shares subject to such Award or so surrendered, as the case may be, to the extent of such expiration, termination, forfeiture or decrease, shall again be available for award under the Plan. Shares issued under the Plan may consist in whole or in part of authorized but unissued shares or treasury shares. No Incentive Stock Option may be issued after the following dates: (x) January 6, 2010 with respect to the 1,000,000 shares of the Company’s Common Stock authorized for issuance hereunder approved by the stockholders of the Company on February 24, 2000; (y) December 13, 2011 with respect to the additional 5,000,000 shares of the Company’s Common Stock authorized for issuance hereunder approved by the stockholders of the Company on May 13, 2002, and (z) January 25, 2016 with respect to the additional 3,000,000 shares of the Company’s Common Stock authorized for issuance hereunder approved by the stockholders of the Company on March 7, 2006.

(b)		In the event that the Committee determines that any stock dividend, recapitalization, reorganization, merger, consolidation, or other similar transaction affects the Common Stock such that an adjustment is required in order to preserve the benefits or potential benefits intended to be made available under the Plan, then the Committee shall equitably adjust any or all of (i) the number and kind of shares in respect of which Awards may be made under the Plan, (ii) the number and kind of shares subject to outstanding Awards, and (iii) the award, exercise or conversion price with respect to any of the foregoing, and if considered by the Committee to be appropriate, the Committee may make provision for a cash payment with respect to an outstanding Award, provided that the number of shares subject to any Award shall always be a whole number.

Section 5. Administration

(a)		The Plan shall be administered by the Committee. Except where the full Board of Directors serves as the Committee, the Committee shall serve at the pleasure of the Board, which may from time to time appoint additional members of the Committee, remove members and appoint new members in substitution for those previously appointed, and fill vacancies however caused. A majority of the Committee shall constitute a quorum and the acts of a majority of the members present at any meeting at which a quorum is present shall be deemed the action of the Committee. To the extent permitted by applicable law, the Committee may delegate (i) to one or more if its members such of its duties, powers and responsibilities as it may determine; (ii) to one or more officers of the Company the power to grant rights or options to the extent permitted by Section 157(c) of the General Corporation Law of the State of Delaware; (iii) to one or more officers of the Company the authority to allocate other Awards among such persons (other than officers of the Company) eligible to receive Awards under the Plan as such delegated officer or officers determine consistent with such delegation, provided, that with respect to any delegation described in this clause (iii), the Committee (or a properly delegated member or members of the Committee) shall have authorized the issuance of a specified number of shares of stock under such Awards and shall have specified the consideration, if any, to be paid therefor; and (iv) to such employees or other persons as it determines such ministerial tasks as it deems appropriate. In the event of any delegation described in the preceding sentence, the term “Committee” shall include the person or persons so delegated to the extent of such delegation.

(b)		Subject to the express provisions of this Plan and provided that all actions taken shall be consistent with the purposes of the Plan, the Committee shall have full and complete authority and the sole discretion to: (i) determine those persons eligible under Section 3; (ii) select those

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		persons to whom Awards shall be granted under the Plan; (iii) determine the time or times when Awards shall be granted; (iv) establish the terms and conditions upon which Awards may be exercised; (v) alter any restrictions or conditions upon any Awards; and (vi) adopt rules and regulations, establish, define and/or interpret any other terms and conditions, and make all other determinations (which may be on a case-by-case basis) deemed necessary or desirable for the administration of the Plan.

(c)		The Terms of each type of Award need not be identical, and the Committee need not treat Participants uniformly. Except as otherwise provided by the Plan or a particular Award, any determination with respect to an Award may be made by the Committee at the time of Award or at any time thereafter.

(d)		In making its determinations hereunder, the Committee shall take into account the nature of the services rendered or to be rendered by the Participant, their present and potential contributions to the success of the Company, and such other factors as the Committee, in its discretion, shall deem relevant in order to accomplish the purposes of the Plan.

Section 6. Stock Options

(a)		General. Subject to the provisions of the Plan, the Committee may award Incentive Stock Options and Non-Qualified Stock Options and determine the number of shares to be covered by each Option, the option price therefore and the conditions and limitations applicable to the exercise of the Option. Any Option granted under this Plan shall be upon such terms and conditions not inconsistent with this Plan as the Committee may determine. At the time of grant of any Option, the Committee shall specify whether the Option is intended to be an Incentive Stock Option or a Non-Qualified Stock Option.

(b)		Price. The price at which any shares of Stock may be purchased pursuant to the exercise of an Option shall be determined by the Committee but may not be less than the greater of (i) the minimum legal consideration required under the laws of the jurisdiction in which the Company is then organized or (ii) the Fair Market Value of the Stock on the date of grant of the Option.

(c)		Re-pricing. The Committee shall not reprice an Option once it has been granted under this Plan by reducing the exercise price of the Option or canceling an Option and regranting a new Option for a similar number of shares at a lower price, except as expressly provided in Section 11(f), (g) or (h).

(d)		Period of Option. Each Option granted under this Plan shall continue in effect for such period not exceeding seven years as the Committee shall determine.

(e)		Exercise of Options:

	(i)		Options may be exercised in whole or in part at such time and in such manner as the Committee may determine.

	(ii)		The purchase price of shares of Stock upon exercise of an Option shall be paid by the Option holder in full upon exercise and may be paid as the Committee may determine in its sole discretion in any combination of: (i) cash or check acceptable to the Committee and payable to the order of the Company; (ii) delivery of shares of Common Stock (valued at Fair Market Value at the date of

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			purchase of the Common Stock subject to the Option); or (iii) such other means as the Committee may permit; provided, however, that payment of the exercise price by delivery of shares of Common Stock of the Company owned by the Option holder may be made only if such payment does not result in a charge to earnings for financial accounting purposes, as determined by the Committee.

	(iii)		With the consent of the Committee, payment of the exercise price may also be made by delivery of a properly executed exercise notice to the Company, together with a copy of irrevocable instructions to a broker to deliver promptly to the Company the payment to pay the exercise price. To facilitate such arrangements, the Company may enter into agreements for coordinating procedures with one or more securities brokerage firms. The date of delivery of such exercise notices shall be deemed the date of exercise.

	(iv)		The Committee may impose such conditions with respect to the exercise of Options, including conditions relating to applicable federal or state securities laws, as it considers necessary or advisable, including making the Common Stock issued upon exercise subject to restrictions on vesting or transferability, or to risk of forfeiture, upon the happening of such events as the Committee may determine, any of which may be accelerated or waived in the Committee’s sole discretion.

	(v)		No shares of Common Stock shall be issued upon exercise of any Option under this Plan until full payment in the form approved by the Committee has been made and all other legal requirements applicable to the issuance or transfer of such shares and such other requirements as are consistent with the Plan have been complied with to the satisfaction of the Committee.

Section 7. Stock Appreciation Rights

(a)		Subject to the provisions of the Plan, the Committee may grant Awards under the Plan of Stock Appreciation Rights to Participants.

(b)		The base value from which appreciation is to be measured for a Stock Appreciation Right shall be an amount (payable in cash or stock) determined by the Committee, but in no event shall such amount be less than the greater of (i) the Fair Market Value of a share of Common Stock on the date the Stock Appreciation Right is granted or (ii) the minimum amount permitted by applicable laws, rules or policies of any regulatory authority or stock exchange. Each Stock Appreciation Right granted shall entitle a Participant upon exercise to an amount equal to (i) excess of (A) the Fair Market Value on the exercise date of one share of Common Stock over (B) the base value from which appreciation is to be measured, times (ii) the number of shares of Common Stock covered by the exercisable portion of the Stock Appreciation Right. Stock Appreciation Rights may be exercised from time to time upon actual receipt by the Company of written notice of exercise stating the portion of the Stock Appreciation Right that is being exercised. No fractional shares will be issued in payment for Stock Appreciation Rights. If there are fractional shares, then such fractional shares shall be rounded down to the next whole share.

(c)		The Company may impose, in its sole discretion, such conditions upon the exercisability or transferability of Stock Appreciation Rights as it may deem fit. A Stock Appreciation Right

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shall expire on a date designated by the Committee that is not later than seven years after the date of grant of the Stock Appreciation Right.

Section 8. Performance Awards

(a)		Subject to the provisions of the Plan, the Committee may grant Awards of Performance Awards and determine the number of such shares for each Performance Cycle and the duration of each Performance Cycle. There may be more than one Performance Cycle in existence at any one time, and the duration of Performance Cycles may differ from each other. The payment value of Performance Awards shall be equal to the product of (A) the number of shares granted times (B) the Fair Market Value of the Common Stock on the date the Performance Awards are earned or, in the discretion of the Committee, on the date the Committee determines that the Performance Awards have been earned.

(b)		The Committee shall establish performance goals for each Performance Cycle for the purpose of determining the extent to which Performance Awards awarded for such Performance Cycle are earned, on the basis of such criteria and to accomplish such objectives as the Committee may from time to time select. During any Performance Cycle, the Committee may adjust the performance goals for such Performance Cycle as it deems equitable in recognition of unusual or non-recurring events affecting the Company, changes in applicable tax laws or accounting principles, or such other factors as the Committee may determine.

(c)		As soon as practicable after the end of a Performance Cycle, the Committee shall determine the number of Performance Awards which have been earned on the basis of the Participant’s satisfaction of established performance goals. The payment values of earned Performance Awards shall be distributed to the Participant or, if the Participant has died, to the Participant’s Designated Beneficiary, as soon as practicable after the Committee’s determination. The Committee shall determine, at or after the time the Award is granted, whether payment values will be settled in whole or in part in cash or other property, including Common Stock.

Section 9. Restricted Stock

(a)		Subject to the provisions of the Plan, the Committee may grant an Award of Restricted Stock and determine the duration of the Restricted Period during which, and the conditions under which, the shares of Restricted Stock may be forfeited to the Company and the other terms and conditions of such Awards. Shares of Restricted Stock may be issued for no cash consideration or such minimum consideration as may be required by applicable law.

(b)		Shares of Restricted Stock may not be sold, assigned, transferred, pledged or otherwise encumbered, except as permitted by the Committee, during the Restricted Period. Shares of Restricted Stock shall be evidenced in such manner as the Committee may determine. Any certificates issued in respect of shares of Restricted Stock shall be registered in the name of the Participant and unless otherwise determined by the Committee, deposited by the Participant, together with a stock power endorsed in blank, with the Company. At the expiration of the Restricted Period, the Company shall deliver such certificates to the Participant or if the Participant has died, to the Participant’s Designated Beneficiary.

Section 10. Stock Units

(a)		Subject to the provisions of the Plan, the Committee may grant Awards of Stock Units subject to such terms, restrictions, conditions, performance criteria, vesting requirements and payment rules as the Committee shall determine.

(b)		Shares of Common Stock awarded in connection with an Award of Stock Units shall be issued for no cash consideration or such minimum consideration as may be required by applicable law.

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Section 11. General Provisions Applicable to Awards

(a)		Documentation. Each Award under the Plan shall be evidenced by a written document delivered to the Participant specifying the terms and conditions thereof and containing such other terms and conditions not inconsistent with the provisions of the Plan as the Committee considers necessary or advisable to achieve the purposes of the Plan or comply with applicable tax and regulatory laws and accounting principles. The date of Award hereunder shall be the date upon which such Award is voted by the Committee, unless such vote provides otherwise.

(b)		Committee Discretion. Each type of Award may be made alone, in addition to or in relation to any other type of Award. Except as otherwise provided by the Plan or a particular Award, any determination with respect to an Award may be made by the Committee at the time of award or at any time thereafter.

(c)		Settlement. The Committee shall determine whether Awards are settled in whole or in part in cash, Common Stock, other securities of the Company, Awards or other property.

(d)		Additional Provisions For Awards: The following additional conditions shall apply to all Awards, as applicable:

	(i)		Incentive Stock Options shall be granted only to employees of the Company or of a “parent corporation” or “subsidiary corporation” (as those terms are defined in Section 424 of the Code) with respect to the Company;

	(ii)		Each Award shall, by its terms, be transferable by the Participant only by will or the laws of descent and distribution, and shall be exercisable only by such Participant during his lifetime; and

	(iii)		The terms and conditions of Incentive Stock Options shall be subject to and comply with Section 422 of the Code, or any successor provision, and any regulations thereunder.

(e)		Termination of Employment. Except as provided herein, the Committee shall determine the effect on an Award of the disability, death, retirement or other termination of employment of a Participant and the extent to which, and the period during which, the Participant’s legal representative, guardian or Designated Beneficiary may receive payment of an Award or exercise rights thereunder.

(f)		Consolidation or Mergers. With respect to Awards granted prior to March 7, 2006, if the Company is to be consolidated with or acquired by another entity in a merger, sale of all or substantially all of the Company’s assets or otherwise (an “Acquisition”), the Committee or the board of directors of any entity assuming the obligations of the Company hereunder shall, as to outstanding Awards, make appropriate provision for the continuation of such Awards by substituting on an equitable basis for the shares then subject to such Awards the consideration payable with respect to the outstanding shares of Common Stock in connection with the Acquisition and by adjusting on an equitable basis the exercise price of such Awards to reflect such Acquisition.

(g)		Recapitalization or Reorganization. With respect to Awards granted prior to March 7, 2006, in the event of a recapitalization or reorganization of the Company (other than an Acquisition) pursuant to which securities of the Company or of another corporation are issued with respect to the outstanding shares of Common Stock, a Participant upon exercising rights under an Award

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shall be entitled to receive what he would have received if he had exercised prior to such recapitalization or reorganization.

(h)

Mergers, etc. With respect to Awards granted on or after March 7, 2006, except as otherwise provided in an Award, the following provisions shall apply in the event of a Covered Transaction:

(i) Assumption or Substitution. If the Covered Transaction is one in which there is an acquiring or surviving entity, the Committee may provide for the assumption of some or all outstanding Awards or for the grant of new awards in substitution therefor by the acquiror or survivor or an affiliate of the acquiror or survivor.

(ii) Cash-Out of Awards. If the Covered Transaction is one in which holders of Stock will receive upon consummation a payment (whether cash, non-cash or a combination of the foregoing), the Committee may provide for payment (a “cash-out”), with respect to some or all Awards (or portion of Awards), equal in the case of each affected Award to the excess, if any, of (A) the fair market value of one share of Stock (as determined by the Committee in its reasonable discretion) times the number of shares of Stock subject to the Award or portion of the Award, over (B) the aggregate exercise or purchase price, if any, under the Award or portion of the Award (in the case of a Stock Appreciation Right, the aggregate base price above which appreciation is measured), in each case on such payment terms (which need not be the same as the terms of payment to holders of Stock) and other terms, and subject to such conditions, as the Committee determines.

(iii) Other Actions. If the Covered Transaction (whether or not there is an acquiring or surviving entity) is one in which there is no assumption, substitution or cash-out, each Award requiring exercise will cease to be exercisable after such payment or other consideration, if any, as the Committee deems equitable in the circumstances, as of the effective time of the Covered Transaction.

(iv) Termination of Awards Upon Consummation of Covered Transaction. Each Award (unless assumed pursuant to Section 11(h)(i) above), other than outstanding shares of Restricted Stock (which shall be treated in the same manner as other shares of Stock, subject to Section 11(h)(v) below), will terminate upon consummation of the Covered Transaction.

(v) Additional Limitations. Any share of Stock delivered pursuant to Section 11(h)(ii) or Section 11(h)(iii) above with respect to an Award may, in the discretion of the Committee, contain such restrictions, if any, as the Committee deems appropriate to reflect any performance or other vesting conditions to which the Award was subject. In the case of Restricted Stock, the Committee may require that any amounts delivered, exchanged or otherwise paid in respect of such Stock in connection with the Covered Transaction be placed in escrow or otherwise made subject to such restrictions as the Committee deems appropriate to carry out the intent of the Plan.

(i)

Modification of Incentive Stock Options. Notwithstanding the foregoing, any adjustments made pursuant to subparagraphs (f) or (g) with respect to Incentive Stock Options shall be made only after the Committee, after consulting with counsel for the Company, determines whether such adjustments would constitute a “modification” of such Incentive Stock Options (as that term is defined in Section 424 of the Code) or would cause any adverse tax consequences for the holders of such Incentive Stock Options. If the Committee determines that such adjustments

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made with respect to Incentive Stock Options would constitute a modification of such Incentive Stock Options, it may refrain from making such adjustments.

(j)		Withholding. The Participant shall pay to the Company, or make provision satisfactory to the Committee for payment of, any taxes required by law to be withheld in respect of Awards under the Plan no later than the date of the event creating the tax liability. In the Committee’s discretion, such tax obligations may be paid in whole or in part in shares of Common Stock, including shares retained from the Award creating the tax obligation, valued at their Fair Market Value on the date of delivery. The Company and its Affiliates may, to the extent permitted by law, deduct any such tax obligations from any payment of any kind otherwise due to the Participant.

(k)		Amendment of Award. The Committee may amend, modify or terminate any outstanding Award, including substituting therefor another Award of the same or a different type, changing the date of exercise or realization, provided that the Participant’s consent to such action shall be required unless the Committee determines that the action, taking into account any related action, would not materially and adversely affect the Participant.

Section 12. Miscellaneous

(a)		No Right To Employment. No person shall have any claim or right to be granted an Award, and the grant of an Award shall not be construed as giving a Participant the right to continued employment. The Company expressly reserves the right at any time to dismiss a Participant free from any liability or claim under the Plan, except as expressly provided in the applicable Award.

(b)		No Rights As Shareholder. Subject to the provisions of the applicable Award, no Participant or Designated Beneficiary shall have any rights as a shareholder with respect to any shares of Common Stock to be distributed under the Plan until he or she becomes the holder thereof. A Participant to whom Common Stock is awarded shall be considered the holder of the Stock at the time of the Award except as otherwise provided in the applicable Award.

(c)		Term of Plan. This Plan shall terminate on January 25, 2016, and no Award shall be granted under this Plan thereafter, but such termination shall not affect the validity of Awards granted prior to the date of termination.

(d)		Amendment of Plan. The Board or Committee, if so authorized by the Board, may amend, suspend or terminate the Plan or any portion thereof at any time.

(e)		Foreign Participants. Subject to the limitations set forth in Section 4 herein, the Committee may grant Awards to Participants who reside or are employed outside the United States on such terms and conditions as determined in the sole discretion of the Committee are necessary or advisable to achieve the purposes of the Plan or to comply with foreign laws, including the establishment of subplans under this Plan. Any subplans or other modifications to Plan terms, conditions or procedures established under this Section, shall be attached as Appendices.

(f)		Governing Law. The provisions of the Plan shall be governed by and interpreted in accordance with the laws of the State of Delaware.

(g)		Indemnity. Neither the Board nor the Committee, nor any members of either, nor any employees of the Company or any parent, subsidiary, or other affiliate, shall be liable for any act, omission, interpretation, construction or determination made in good faith in connection with their responsibilities with respect to this Plan, and the Company hereby agrees to indemnify the members of the Board, the members of the Committee, and the employees of the Company and its parent or subsidiaries in respect of any claim, loss, damage, or expense

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(including reasonable counsel fees) arising from any such act, omission, interpretation, construction or determination to the full extent permitted by law.

(h)		Section 409A. Notwithstanding anything to the contrary in this Plan or any Award, these provisions shall apply to any payments and benefits otherwise payable to or provided to a Participant under this Plan and any Award. For purposes of Section 409A of the Code, each “payment” (as defined by Section 409A of the Code) made under this Plan or an Award shall be considered a “separate payment.” In addition, for purposes of Section 409A of the Code, payments shall be deemed exempt from the definition of deferred compensation under Section 409A of the Code to the fullest extent possible under (i) the “short-term deferral” exemption of Treasury Regulation § 1.409A-1(b)(4), and (ii) (with respect to amounts paid as separation pay no later than the second calendar year following the calendar year containing the participant’s “separation from service” (as defined for purposes of Section 409A of the Code)) the “two years/two-times” separation pay exemption of Treasury Regulation § 1.409A-1(b)(9)(iii), which are hereby incorporate by reference.

		If a participant is a “specified employee” as defined in Section 409A of the Code (and as applied according to procedures of the Company and its affiliates) as of his separation from service, to the extent any payment under this Plan or an Award constitutes deferred compensation (after taking into account any applicable exemptions from Section 409A of the Code), and to the extent required by Section 409A of the Code, no payments due under this Plan or an Award may be made until the earlier of: (i) the first day of the seventh month following the Participant’s separation from service, or (ii) the Participant’s date of death; provided, however, that any payments delayed during this six-month period shall be paid in the aggregate in a lump sum, without interest, on the first day of the seventh month following the Participant’s separation from service.

		The Committee shall administer the Plan with a view toward ensuring that Awards under the Plan that are subject to Section 409A of the Code comply with the requirements thereof and that Options and SARs under the Plan be exempt from the requirements of Section 409A of the Code, but neither the Committee nor any member of the Board, nor the Company nor any of its affiliates, nor any other person acting hereunder on behalf of the Company, the Committee or the Board shall be liable to a Participant or any Designated Beneficiary by reason of the acceleration of any income, or the imposition of any additional tax or penalty, with respect to an Award, whether by reason of a failure to satisfy the requirements of Section 409A of the Code or otherwise.

Dates of Approval by Board of Directors or Compensation Committee: January 6, 2000, January 23, 2001, and December 13, 2001, May 20, 2002, September 13, 2002, February 26, 2003, February 25, 2004, January 25, 2006, May 6, 2008 and December 29, 2008.

Dates of Approval by Stockholders: February 24, 2000, February 28, 2001, May 13, 2002, April 27, 2004, March 7, 2006 and May 6, 2008.

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EX-31.01 3 b73889baexv31w01.htm EX-31.01 RULE 13A-14(A), 15D-14(A) CERTIFICATION exv31w01

EXHIBIT 31.01

CERTIFICATION PURSUANT TO SECTION 302 OF THE SARBANES-OXLEY ACT OF 2002

I, Robert J. Lepofsky, certify that:

1.		I have reviewed this quarterly report on Form 10-Q of Brooks Automation, Inc.;

2.		Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3.		Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4.		The registrant’s other certifying officer and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

a.		Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b.		Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c.		Evaluated the effectiveness of the registrant’s disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d.		Disclosed in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting; and

5.		The registrant’s other certifying officer and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant’s auditors and the audit committee of the registrant’s board of directors (or persons performing the equivalent functions):

a.		All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant’s ability to record, process, summarize and report financial information; and

b.		Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s internal control over financial reporting.



/s/ Robert J. Lepofsky
Robert J. Lepofsky
President and Chief Executive Officer

Date: February 9, 2009

EX-31.02 4 b73889baexv31w02.htm EX-31.02 RULE 13A-14(A), 15D-14(A) CERTIFICATION exv31w02

EXHIBIT 31.02

CERTIFICATION PURSUANT TO SECTION 302 OF THE SARBANES-OXLEY ACT OF 2002

I, Martin S. Headley, certify that:

1.		I have reviewed this quarterly report on Form 10-Q of Brooks Automation, Inc.;

2.		Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3.		Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4.		The registrant’s other certifying officer and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

a.		Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b.		Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c.		Evaluated the effectiveness of the registrant’s disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d.		Disclosed in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting; and

5.		The registrant’s other certifying officer and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant’s auditors and the audit committee of the registrant’s board of directors (or persons performing the equivalent functions):

a.		All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant’s ability to record, process, summarize and report financial information; and

b.		Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s internal control over financial reporting.



/s/ Martin S. Headley
Martin S. Headley
Executive Vice President and Chief Financial Officer

Date: February 9, 2009

EX-32 5 b73889baexv32.htm EX-32 SECTION 1350 CERTIFICATION exv32

EXHIBIT 32

CERTIFICATION

Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002 (Subsections (a) and (b) of Section 1350, Chapter 63 of Title 18, United States Code)

Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002 (subsections (a) and (b) of Section 1350, Chapter 63 of Title 18, United States Code), the undersigned officer of Brooks Automation, Inc., a Delaware corporation (the “Company”), does hereby certify, to the best of such officer’s knowledge and belief, that:

(1) The Quarterly Report on Form 10-Q for the quarter ended December 31, 2008 of the Company fully complies with the requirements of Section 13(a) or 15(d) of the Securities Exchange Act of 1934; and

(2) The information contained in this Form 10-Q fairly presents, in all materials respects, the financial condition and results of operations of the Company.



Dated: February 9, 2009	/s/ Robert J. Lepofsky
	Robert J. Lepofsky
	President and Chief Executive Officer (Principal Executive Officer)


Dated: February 9, 2009	/s/ Martin S. Headley
	Martin S. Headley
	Executive Vice President and Chief Financial Officer (Principal Financial Officer)

A signed original of this written statement required by Section 906 has been provided to Brooks Automation, Inc. and will be retained by Brooks Automation, Inc. and furnished to the Securities and Exchange Commission or its staff upon request.

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