8-K

UNITED STATES
SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 8-K

CURRENT REPORT

PURSUANT TO SECTION 13 OR 15(d) OF THE
SECURITIES EXCHANGE ACT OF 1934

Date of report (Date of earliest event reported): August 6, 2009

BROOKS AUTOMATION, INC.

(Exact name of registrant as specified in its charter)

DELAWARE

(State or other jurisdiction of incorporation)

0-25434	04-3040660
(Commission File Number)	(IRS Employer Identification No.)
15 Elizabeth Drive, Chelmsford, MA	01824
(Address of principal executive offices)	(Zip Code)

Registrant’s telephone number, including area code (978) 262-2400.

Check the appropriate box below if the Form 8-K filing is intended to simultaneously satisfy the filing obligation of the registrant under any of the following provisions:

o     Written communications pursuant to Rule 425 under the Securities Act (17 CFR 230.425)

o     Soliciting material pursuant to Rule 14a-12 under the Exchange Act (17 CFR 240.14a-12)

o     Pre-commencement communications pursuant to Rule 14d-2(b) under the Exchange Act (17 CFR 240.14d-2(b))

o     Pre-commencement communications pursuant to Rule 13e-4(c) under the Exchange Act (17 CFR 240.13e-4(c))

TABLE OF CONTENTS

	ITEM 2.02 RESULTS OF OPERATIONS AND FINANCIAL CONDITION
	ITEM 9.01 FINANCIAL STATEMENTS AND EXHIBITS
SIGNATURES
EXHIBIT INDEX
Ex-99.1 Press Release issued on August 6, 2009
Ex-99.2 Investor Conference Call Slide Presentation

ITEM 2.02 RESULTS OF OPERATIONS AND FINANCIAL CONDITION

On August 6, 2009, Brooks Automation, Inc. (“Brooks” or the “Company”) announced via press release its financial results for the fiscal quarter ended June 30, 2009. A copy of the press release is attached hereto as Exhibit 99.1.

In connection with the conference call held by the Company on August 6, 2009 to discuss its financial results for the fiscal quarter ended June 30, 2009, the Company referenced a slide presentation, which was made available in advance of the call through the Company’s website. The slide presentation is attached as Exhibit 99.2 hereto.

Limitation on Incorporation by Reference. The information in this Item 2.02 and in Item 9.01 of this Current Report, including the exhibits attached hereto, shall not be deemed “filed” for purposes of Section 18 of the Securities Exchange Act of 1934, as amended, or otherwise subject to the liabilities of that section, nor shall such information be deemed incorporated by reference in any filing under the Securities Act of 1933, as amended, except as shall be expressly set forth by specific reference in such a filing.

Cautionary Note Regarding Forward-Looking Statements. Except for historical information contained in this press release attached as an exhibit hereto, the press release contains forward-looking statements which involve certain risks and uncertainties that could cause actual results to differ materially from those expressed or implied by these statements. Please refer to the cautionary note in the press release regarding these forward-looking statements.

ITEM 9.01 FINANCIAL STATEMENTS AND EXHIBITS

(d) Exhibits

99.1	Press release issued on August 6, 2009 by Brooks Automation, Inc., announcing its financial results for the fiscal quarter ended June 30, 2009.
99.2	Investor Conference Call Slide Presentation.

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 hereunto duly authorized.

BROOKS AUTOMATION, INC.
 

/s/ Thomas S. Grilk  

Thomas S. Grilk 

Senior Vice President, General Counsel and
Secretary 

Date: August 6, 2009

EXHIBIT INDEX

Exhibit No.	Description
99.1	Press release issued on August 6, 2009 by Brooks Automation, Inc., announcing its financial results for the fiscal quarter ended June 30, 2009.
99.2	Investor Conference Call Slide Presentation.

EX-99.1

Exhibit 99.1

Press Release

For Immediate Release
August 6, 2009

Brooks Automation Reports THIRD Quarter Financial Results

Chelmsford, Massachusetts August 6, 2009 — Brooks Automation, Inc. (Nasdaq: BRKS) announced financial results for the Company’s third quarter of fiscal year 2009 ended on June 30, 2009.

Revenues for the third quarter of 2009 were $43.9 million, compared to revenues of $124.0 million in the third quarter of 2008, a decrease of 64.6%. Sequentially, revenues grew 17.6% from second quarter revenues of $37.3 million.

Net loss for the third quarter of fiscal 2009 amounted to $25.7 million, or $0.41 per diluted share. Excluding special charges totaling $2.7 million, the non-GAAP net loss for the third quarter of fiscal 2009 was $23.0 million, or $0.37 per diluted share. The special charges taken during the quarter were $2.3 million of restructuring charges, primarily for severance and $0.4 million of asset impairments associated with closing one of the company’s facilities.

The fiscal 2009 third quarter results compare with a net loss from continuing operations of $10.3 million, or $0.17 per diluted share in the third quarter of the prior year. Sequentially, the net loss was $152.5 million or $2.43 per diluted share in the second quarter of 2009. Excluding special charges, the net loss from continuing operations for the third quarter of the prior year was $7.8 million, or $0.12 per diluted share. Sequentially, the net loss for the second quarter excluding special charges, was $36.2 million or $0.58 per diluted share. Special charges are identified in the tables to this release.

Adjusted Earnings (Loss) before Interest, Tax, Depreciation and Amortization for the third quarter of fiscal 2009 was ($17.2) million, which compared to $1.8 million in the prior year period and ($26.7) million in the second quarter of fiscal 2009. Effective working capital management and reduced levels of losses reduced the sequential use of cash for operations to $16.0 million during the quarter. The Company closed the quarter with $114.4 million of cash and marketable securities.

Revenues for the nine months ended June 30, 2009 were $154.6 million, a 63.1% decrease from the prior period revenues of $419.5 million. The loss from continuing operations for the current fiscal nine month period was $213.4 million, as compared to the prior year’s net loss of $20.4 million. Excluding special charges of $124.4 million in the current fiscal year and $8.6 million in the prior year, the loss from continuing operations before special charges was $89.0 million or $1.42 per share and $11.8 million or $0.18 per share, respectively. Special charges are identified in the tables to this release.

— more —

Brooks Automation, Inc. w15 Elizabeth Drive w Chelmsford, Massachusetts 01824 w (978)262-2400 w www.brooks.com.

Brooks Automation Reports third Quarter Financial Results...................page two

Commenting on recent activities, Robert J. Lepofsky, President and Chief Executive Officer of Brooks stated, “We have experienced accelerating revenue growth as the quarter progressed which, combined with the benefits of our restructuring activities, narrowed the losses during the quarter. We see continuing momentum, particularly for our semiconductor business, and our internal plans are for sequential revenue growth of at least 25% in the September ending quarter. In addition, our use of cash continues to substantially diminish as we maintain our focus on working capital management programs and we move beyond the use of cash for restructuring and IT investments. We are delivering the expected high drop-thru on every incremental dollar of revenue as projected in our business model which will accelerate our return to profitability. The recovery in the semiconductor capital equipment industry is progressing and Brooks’ leadership position as a strategic extension of our customer’s engineering, manufacturing and product support capabilities is clearly strengthening. With increasing revenues, important design-in wins, the improving utilization rates of existing wafer fabs driving our Global Customer Operations business, and the expected returns from our product development initiatives across multiple market sectors, we believe Brooks will emerge from the current business downturn very well positioned to deliver excellent returns to our shareholders.”

A reconciliation of non-GAAP measures to the most nearly comparable GAAP measure follows the consolidated statements of operations, balance sheets and statements of cash flows attached to this release.

Brooks management will webcast its June quarter earnings conference call on Thursday, August 6, 2009 at 4:30 p.m. Eastern Time to discuss the attached quarterly results and business highlights. During the call, Company management will respond to questions concerning, but not limited to, the Company’s financial performance, business conditions and industry outlook. Their responses could contain information that has not been previously disclosed.

Analysts, investors and members of the media can access the live broadcast available on Brooks’ website at www.brooks.com. The call will be archived on this website for convenient on-demand replay until Brooks reports fiscal 2009 fourth quarter results in mid-November, 2009.

# # #

About Brooks Automation, Inc.

Brooks is a leading worldwide provider of automation, vacuum and instrumentation solutions to the global semiconductor and related industries. The company’s advanced offerings in hardware and services are critical to customers where equipment productivity and availability are essential for successful manufacturing. Brooks’ products and global services are used in virtually every fab in the world as well as in a number of diverse industries outside semiconductor manufacturing. For more information see www.brooks.com or email co.csr@brooks.com.

Brooks Automation, Inc. w 15 Elizabeth Drive w Chelmsford, Massachusetts 01824 w (978)262-2400 w www.brooks.com.

Brooks Automation Reports Third Quarter Financial Results..................page three

“Safe Harbor Statement” under Section 21E of the Securities Exchange Act of 1934

Some statements in this release are forward-looking statements made under Section 21E of the Securities Exchange Act of 1934. These statements are neither promises nor guarantees but involve risks and uncertainties, both known and unknown, that could cause Brooks’ financial and business results to differ materially from our expectations. They are based on the facts known to management at the time they are made. These forward-looking statements include statements regarding our profit and loss and cash flow expectations and our ability to achieve financial success in the future. Factors that could cause results to differ from our expectations include the following: volatility of the industries the Company serves, particularly the semiconductor industry; our possible inability to meet increased demand for our products due to difficulties in obtaining components and materials from our suppliers in required quantities and of required quality; the inability of customers to make payments to us when due; the timing and effectiveness of cost reduction and cost control measures; intense price competition; disputes concerning intellectual property; expenses associated with legal disputes and litigation, continuing uncertainties in global political and economic conditions, the impact of global health concerns, and other factors and other risks that we have described in our filings with the Securities and Exchange Commission, including but not limited to our Annual Report on Form 10-K, current reports on Form 8-K and our quarterly reports on Form 10-Q. As a result we can provide no assurance that our future results will not be materially different from those projected. Brooks expressly disclaims any obligation or undertaking to release publicly any updates or revisions to any such statement to reflect any change in our expectations or any change in events, conditions or circumstances on which any such statement is based. Brooks undertakes no obligation to update the information contained in this press release.

Contact:
Barbara Culhane
Corporate Marketing Manager
Brooks Automation, Inc.
978-262-2400
www.brooks.com

Brooks Automation, Inc. w 15 Elizabeth Drive w Chelmsford, Massachusetts 01824 w (978)262-2400 w www.brooks.com.

BROOKS AUTOMATION, INC.
CONSOLIDATED STATEMENTS OF OPERATIONS
(unaudited)
(In thousands, except per share data)

	Three months ended						Nine months ended
	June 30,						June 30,
	2009			2008			2009			2008
Revenues
Product	$	31,510		$	105,774		$	116,479		$	367,157
Services		12,366			18,242			38,142			52,339
Total revenues		43,876			124,016			154,621			419,496
Cost of revenues
Product		29,301			78,308			115,078			266,798
Services		10,617			16,851			36,477			48,953
Impairment of long-lived assets		408			—			20,924			—
Total cost of revenues		40,326			95,159			172,479			315,751
Gross profit (loss)		3,550			28,857			(17,858	)		103,745
Operating expenses
Research and development		7,549			10,270			24,492			34,255
Selling, general and administrative		19,559			25,636			72,400			84,635
Impairment of goodwill		—			—			71,800			—
Impairment of long-lived assets		—			—			14,588			—
Restructuring charges		2,327			2,571			12,293			5,677
Total operating expenses		29,435			38,477			195,573			124,567
Operating loss from continuing operations		(25,855	)		(9,620	)		(213,431	)		(20,822	)
Interest income		536			1,237			2,079			6,252
Interest expense		60			93			258			536
Loss on investment		—			—			1,185			2,931
Other (income) expense, net		(114	)		1,244			35			426
Loss from continuing operations before income taxes and minority interests		(25,295	)		(9,720	)		(212,830	)		(18,463	)
Income tax provision		148			843			728			2,398
Loss from continuing operations before minority interests		(25,443	)		(10,563	)		(213,558	)		(20,861	)
Minority interests in income of consolidated subsidiaries		240			(13	)		63			(5	)
Equity in earnings of joint ventures		(59	)		224			253			447
Loss from continuing operations		(25,742	)		(10,326	)		(213,368	)		(20,409	)
Gain on sale of discontinued operations, net of income taxes		—			—			—			371
Income from discontinued operations, net of income taxes		—			—			—			371
Net loss	$	(25,742	)	$	(10,326	)	$	(213,368	)	$	(20,038	)
Basic loss per share from continuing operations	$	(0.41	)	$	(0.17	)	$	(3.40	)	$	(0.31	)
Basic income per share from discontinued operations		—			—			—			0.01
Basic net loss per share	$	(0.41	)	$	(0.17	)	$	(3.40	)	$	(0.31	)
Diluted loss per share from continuing operations	$	(0.41	)	$	(0.17	)	$	(3.40	)	$	(0.31	)
Diluted income per share from discontinued operations		—			—			—			0.01
Diluted net loss per share	$	(0.41	)	$	(0.17	)	$	(3.40	)	$	(0.31	)
Shares used in computing income (loss) per share
Basic		63,011			62,483			62,835			65,196
Diluted		63,011			62,483			62,835			65,196

Brooks Automation, Inc. w 15 Elizabeth Drive w Chelmsford, Massachusetts 01824 w (978)262-2400 w www.brooks.com.

BROOKS AUTOMATION, INC.
CONSOLIDATED BALANCE SHEETS
(unaudited)
(In thousands, except share and per share data)

	June 30,			September 30,
	2009			2008
Assets
Current assets
Cash and cash equivalents	$	52,936		$	110,269
Marketable securities		35,313			33,077
Accounts receivable, net		28,108			66,844
Insurance receivable for litigation		343			8,772
Inventories, net		91,404			105,901
Prepaid expenses and other current assets		9,149			13,783
Total current assets		217,253			338,646
Property, plant and equipment, net		78,393			81,604
Long-term marketable securities		26,159			33,935
Goodwill		48,138			119,979
Intangible assets, net		14,909			58,452
Equity investment in joint ventures		28,730			26,309
Other assets		3,502			4,713
Total assets	$	417,084		$	663,638
Liabilities, minority interests and stockholders’ equity
Current liabilities
Accounts payable	$	15,700		$	37,248
Deferred revenue		2,884			3,553
Accrued warranty and retrofit costs		5,621			8,174
Accrued compensation and benefits		13,071			18,174
Accrued restructuring costs		8,030			7,167
Accrued income taxes payable		2,702			3,151
Accrual for litigation settlement		—			7,750
Accrued expenses and other current liabilities		14,063			17,634
Total current liabilities		62,071			102,851
Accrued long-term restructuring		2,707			5,496
Income taxes payable		10,649			10,649
Long-term pension liability		6,243			—
Other long-term liabilities		2,699			2,238
Total liabilities		84,369			121,234
Contingencies Minority interests		471			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, 77,740,154 shares issued and 64,278,285 shares outstanding at June 30, 2009, 77,044,737 shares issued and 63,582,868 shares outstanding at September 30, 2008		777			770
Additional paid-in capital		1,794,287			1,788,891
Accumulated other comprehensive income		16,277			18,063
Treasury stock at cost, 13,461,869 shares at June 30, 2009 and September 30, 2008		(200,956	)		(200,956	)
Accumulated deficit		(1,278,141	)		(1,064,773	)
Total stockholders’ equity		332,244			541,995
Total liabilities, minority interests and stockholders’ equity	$	417,084		$	663,638

Brooks Automation, Inc. w 15 Elizabeth Drive w Chelmsford, Massachusetts 01824 w (978)262-2400 w www.brooks.com.

BROOKS AUTOMATION, INC.
CONSOLIDATED STATEMENTS OF CASH FLOWS
(unaudited)
(In thousands)

	Nine months ended
	June 30,
	2009			2008
Cash flows from operating activities
Net loss	$	(213,368	)	$	(20,038	)
Adjustments to reconcile net loss to net cash provided by (used in) operating activities:
Depreciation and amortization		20,841			25,867
Impairment of goodwill		71,800			—
Impairment of long-lived assets		35,512			—
Stock-based compensation		5,007			5,612
Amortization of discount on marketable securities		70			(782	)
Undistributed earnings of joint ventures		(253	)		(447	)
Minority interests		63			(5	)
(Gain) loss on disposal of long-lived assets		(12	)		925
Loss on investment		1,185			2,931
Gain on sale of software division, net		—			(371	)
Changes in operating assets and liabilities, net of acquisitions and disposals:
Accounts receivable		38,432			32,220
Inventories		14,324			(5,138	)
Prepaid expenses and other current assets		5,199			2,469
Accounts payable		(21,533	)		(18,344	)
Deferred revenue		(658	)		(1,578	)
Accrued warranty and retrofit costs		(2,558	)		(2,454	)
Accrued compensation and benefits		(4,313	)		(6,906	)
Accrued restructuring costs		(1,902	)		(1,356	)
Accrued expenses and other current liabilities		(757	)		(5,974	)
Net cash provided by (used in) operating activities		(52,921	)		6,631
Cash flows from investing activities
Purchases of property, plant and equipment		(10,843	)		(17,235	)
Purchases of marketable securities		(53,316	)		(137,156	)
Sale/maturity of marketable securities		58,903			174,973
Proceeds from sale of software division		—			1,500
Proceeds from the sale of long-lived assets		1,093			—
Purchases of intangible assets		(38	)		(75	)
Net cash provided by (used in) investing activities		(4,201	)		22,007
Cash flows from financing activities
Treasury stock purchases		—			(90,194	)
Proceeds from issuance of common stock, net of issuance costs		675			1,473
Net cash provided by (used in) financing activities		675			(88,721	)
Effects of exchange rate changes on cash and cash equivalents		(886	)		1,813
Net decrease in cash and cash equivalents		(57,333	)		(58,270	)
Cash and cash equivalents, beginning of period		110,269			168,232
Cash and cash equivalents, end of period	$	52,936		$	109,962

Brooks Automation, Inc. w 15 Elizabeth Drive w Chelmsford, Massachusetts 01824 w (978)262-2400 w www.brooks.com.

BROOKS AUTOMATION, INC.

Supplemental Information
(In thousands, except per share data)
(unaudited)

Notes on Non-GAAP Financial Measures:

The information in this press release is for: internal managerial purposes; when publicly providing guidance on future results; and as a means to evaluate period-to-period comparisons. These financial measures are used in addition to and in conjunction with results presented in accordance with GAAP and should not be relied upon to the exclusion of GAAP financial measures. Management believes these financial measures provide an additional way of viewing aspects of our operations, that, when viewed with our GAAP results and the accompanying reconciliations to the corresponding GAAP financial measures, provide a more complete understanding of our business. Management strongly encourages investors to review our financial statements and publicly-filed reports in their entirety and not rely on any single measure.

The press release includes financial measures which exclude the effects of charges associated with our non-cash impairment charges, restructuring programs and gains or losses on investments. Management believes these measures are useful to investors because it eliminates accounting charges that do not reflect Brooks’ day-to-day operations. A table reconciling income (loss) and diluted earnings (loss) per share from continuing operations is presented below:

Brooks Automation, Inc. w 15 Elizabeth Drive w Chelmsford, Massachusetts 01824 w (978)262-2400 w www.brooks.com.

	Quarter ended
	June 30, 2009						March 31, 2009						June 30, 2008
	$			per share			$			per share			$			per share
Loss from continuing operations	$	(25,742	)	$	(0.41	)	$	(152,543	)	$	(2.43	)	$	(10,326	)	$	(0.17	)
Impairment charges — cost of revenues		408			0.01			20,516			0.33			—			—
Impairment charges — operating expense		—			—			86,388			1.37			—			—
Restructuring charges		2,327			0.04			5,861			0.09			2,571			0.04
Restructuring related inventory charges		—			—			3,612			0.06			—			—
Loss on investment		—			—			—			—			—			—
Adjusted loss from continuing operations	$	(23,007	)	$	(0.37	)	$	(36,166	)	$	(0.58	)	$	(7,755	)	$	(0.12	)

	Nine months ended
	June 30, 2009						June 30, 2008
	$			per share			$			per share
Loss from continuing operations	$	(213,368	)	$	(3.40	)	$	(20,409	)	$	(0.31	)
Impairment charges — cost of revenues		20,924			0.33			—			—
Impairment charges — operating expense		86,388			1.37			—			—
Restructuring charges		12,293			0.20			5,677			0.09
Restructuring related inventory charges		3,612			0.06			—			—
Loss on investment		1,185			0.02			2,931			0.04
Adjusted loss from continuing operations	$	(88,966	)	$	(1.42	)	$	(11,801	)	$	(0.18	)

	Quarter ended									Nine months ended
	June 30,			Mar 31,			June 30,			June 30,			June 30,
	2009			2009			2008			2009			2008
Loss from continuing operations	$	(25,742	)	$	(152,543	)	$	(10,326	)		(213,368	)		(20,409	)
Less: Interest income		(536	)		(646	)		(1,237	)		(2,079	)		(6,252	)
Add: Interest expense		60			72			93			258			536
Add: Income tax provision (benefit)		148			189			843			728			2,398
Add: Depreciation		3,679			3,620			4,718			11,455			13,616
Add: Amortization of completed technology		457			2,331			2,331			5,119			6,993
Add; Amortization of acquired intangible assets		381			1,993			1,786			4,267			5,258
Add: Stock compensation expense		1,613			1,870			1,069			5,007			5,612
Add: Restructuring related inventory charges		—			3,612			—			3,612			—
Add: Impairment charges — cost of revenues		408			20,516			—			20,924			—
Add: Impairment charges — operating expense		—			86,388			—			86,388			—
Add: Restructuring charges		2,327			5,861			2,571			12,293			5,677
Add: Loss on investment		—			—			—			1,185			2,931
Adjusted EBITDA	$	(17,205	)	$	(26,737	)	$	1,848		$	(64,211	)	$	16,360

Brooks Automation, Inc. w 15 Elizabeth Drive w Chelmsford, Massachusetts 01824 w (978)262-2400 w www.brooks.com.

EX-99.2

Exhibit 99.2

3rd Quarter Fiscal 2009 Financial Results Conference Call Thursday, August 6, 2009 4:30 p.m. ET

Safe Harbor Statement & Non-GAAP Financial Measures "Safe Harbor" Statement under the U.S. Private Securities Litigation Reform Act of 1995; certain matters in this presentation, including forecasts of future demand and future Company performance, are forward-looking statements that are subject to risks and uncertainties that could cause actual results to materially differ, either better or worse, from those projected. Further discussions of risk factors are available in the Company's most recent SEC filings including form 10-K for the fiscal year ended 9/30/08 The Company assumes no obligation to update the information in this presentation. Financial information in this presentation is for: internal managerial purposes; when publicly providing guidance on future results; and as a means to evaluate period-to- period comparisons. These financial measures are used in addition to and in conjunction with results presented in accordance with GAAP and should not be relied upon to the exclusion of GAAP financial measures. Management believes these financial measures provide an additional way of viewing aspects of our operations, that, when viewed with our GAAP results and the reconciliations to GAAP financial measures, provide a more complete understanding of our business. Management strongly encourages investors to review our financial statements and publicly filed reports in their entirety and not rely on any single measure.

Beyond the Trough $millions Q2 Q3 Change Revenues $ 37.3 $ 43.9 $ 6.6 Gross Profit (Loss) ( 3.7) 4.0 7.7 Research & Development 7.7 7.5 0.2 SG&A, continuing 21.6 18.8 2.8 Equity investigation 3.6 0.8 2.8 Operating Loss before Special Charges ($ 36.5) ($ 23.1) $ 13.4

Semiconductor OEMs lead the way Late quarter pick-up in service and spares revenues $millions Q3 FY08 Q2 FY09 Q3 FY09 9 Semiconductor OEM's $ 53.6 $ 8.5 $ 13.2 Other customers 70.4 28.8 30.7 Total $ 124.0 $37.3 $ 43.9 Semiconductor 72% 65% 70% Industrial 10% 19% 14% Other markets 18% 16% 16%

Q3 reflects initial market rebound and continuing benefits of restructuring program 2nd Quarter Fiscal 2009 $ 37.3 ($ 36.5) Product revenue growth 5.6 5.0 Service revenue growth 1.0 0.7 Lower intangible asset amortization 3.5 Additional Instrumentation R&D investment (0.3) Lower operating expense spend 1.7 Lower equity investigation expenses 2.8 3rd Quarter Fiscal 2009 $ 43.9 ($ 23.1) Revenues Profits before Special Charges

Continued Improvement in Adjusted EBITDA Revenues 73.4 37.3 43.9 Adjusted EBITDA -20.3 -26.7 -17.2 Q1 Q2 Q3

Limited Special charges impact on GAAP Net Income $ millions Q2 Q3 Comments on Sequential Trends Operating loss before Special Charges ($ 36.5) ($ 23.1) Special charges ( 116.4) ( 2.7) Restructuring related expenses in Q3 Interest income, net 0.6 0.5 Other expense ( 0.1) 0.1 Foreign currency fluctuations Income tax provision ( 0.2) ( 0.1) Non- cash tax provisions Minorities & joint ventures 0.1 ( 0.4) Japanese JVs incur small losses Net loss from Continuing Operations ($ 152.5) ($ 25.7)

Cash utilization greatly reduced Adjusted EBITDA ($ 17.2) Restructuring cash flow ( 5.4) Net Interest income 0.5 Change in assets and other 6.1 Cash flow from Continuing Operations ( 16.0) Capital Expenditures ( 1.8) Currency and other 2.0 Net Change in Cash and Marketable Investments ($ 15.8) A reconciliation of Adjusted EBITDA to Brooks' Net Loss is included in the earnings release issued on August 6, 2009 $ millions

Critical Balance Sheet accounts $ millions March 2009 June 2009 Comments on Sequential Trends Cash and Marketable Securities 130.2 114.4 Accounts receivable, net 25.6 28.1 DSO improves by 4 days Inventories, net 98.5 91.4 Gross inventory reduction of $8.1 million Accounts payable ( 16.1) ( 15.7) DPO moved back out 5 days Accrued restructuring costs (current and long term) ( 14.5) ( 10.7)

Critical Solutions Segment $ millions Q2 Q3 Comments on Sequential Trends Revenues $17.2 $16.8 Continued difficulties in industrial markets Gross Profit before amortization & special charges 0.9 1.3 Full quarter impacts of 2nd quarter restructuring activities GAAP Gross Profit ( 0.1) 0.9 Still carrying surplus capacity costs Operating Expenses 13.0 13.4 Increased R&D driven by instrumentation products Segment Operating Loss ($13.1) ($12.5)

Systems Solutions Segment $ millions Q2 Q3 Comments on Sequential Trends Revenues $8.2 $14.2 72% growth led by Extended Factory products Gross Loss before amortization & special charges ( 3.6) 1.1 Volume drop through and benefits of 2nd quarter restructuring activities GAAP Gross Profit (Loss) ( 5.9) 1.1 Still carrying surplus capacity costs Operating Expenses 9.3 7.4 Segment Operating Loss ($15.2) ( $6.3)

Global Customer Operations $ millions Q2 Q3 Comments on Sequential Trends Revenues $11.8 $12.8 9% growth - back end loaded Gross Profit before amortization & special charges 1.4 2.1 Strong variable contribution and benefits of restructuring actions GAAP Gross Profit (Loss) (1.3) 2.0 Reduced intangibles amortization impact Operating Expenses 5.0 5.0 Segment Operating Loss ($6.3) ( $3.0)

Narrowing breakeven gap Q4 FY07 Q1 FY08 Q2 FY08 Q3 FY08 Q4 FY08 Q1 FY09 Q2 FY09 Q3 FY09 Revenues 166.5 147.8 147.6 124 106.9 73.4 37.3 44.3 Breakeven 159.2 146.2 150.7 143.3 125.5 131.6 99.5 93 Adj EBITDA Breakeven 132.8 120.9 124 120.5 102.9 110.1 80 78 Q U A R T E R L Y $ M I L L I O N S

Looking Forward Internal plans for at least 25% revenue growth for the September quarter Profits drop through at least at model levels Inventories continue to reduce through the recovery Cash utilization closing in on breakeven

Q3 Fiscal 2009 Financial Results Conference Call Thursday, August 6, 2009 4:30 p.m. ET