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 4, 2011

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
EX-99.1
EX-99.2

ITEM 2.02 RESULTS OF OPERATIONS AND FINANCIAL CONDITION

On August 4, 2011, Brooks Automation, Inc. (“Brooks” or the “Company”) announced via press release its financial results for the fiscal quarter ended June 30, 2011. A copy of the press release is attached hereto as Exhibit 99.1.

In connection with the conference call to be held by the Company on August 4, 2011 to discuss its financial results for the fiscal quarter ended June 30, 2011, the Company will reference 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 4, 2011 by Brooks Automation, Inc.

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/ Jason Joseph
	Jason Joseph
Date: August 4, 2011	Vice President, General Counsel and Secretary

EXHIBIT INDEX

Exhibit No.		Description
	99.1	Press release issued on August 4, 2011 by Brooks Automation, Inc.
	99.2	Investor Conference Call Slide Presentation.

EX-99.1

Exhibit 99.1

Press Release

For Immediate Release

Brooks Automation Reports Third Quarter Financial Results And Initiates
Payment of A Quarterly Cash Dividend

Chelmsford, Massachusetts August 4, 2011 — Brooks Automation, Inc. (Nasdaq: BRKS) announced financial results for the Company’s third quarter of fiscal year 2011 ended on June 30, 2011.

Revenues for the third quarter of fiscal 2011 were $186.1 million, compared to revenues of $156.8 million in the third quarter of fiscal 2010, an increase of 18.7%. Sequentially, revenues decreased 3.4% from second quarter fiscal 2011 revenues of $192.7 million. Order bookings for the third quarter of fiscal 2011 were $190.8 million, a 1.5% sequential decrease as compared to order bookings in the fiscal second quarter of $193.7 million.

Net income attributable to Brooks Automation, Inc. for the third quarter of fiscal 2011 amounted to $66.2 million, or $1.02 per diluted share. The result included the gain on sale of the contract manufacturing business which resulted in a pre-tax gain of $45.0 million with associated taxes on the gain of $2.4 million. This and other special charges and non-recurring income and their impact on comparative results are identified in the unaudited table included with this release.

Excluding special charges or non-recurring income, the adjusted net income of $23.3 million or $0.36 per diluted share compares on a sequential basis with $26.8 million or $0.41 per diluted share and improves on income of $16.9 million or $0.26 per diluted share in the third quarter of fiscal 2010. Including special charges and non-recurring income, the Net income attributable to Brooks in the second quarter of fiscal 2011 and the third quarter of fiscal 2010 was $26.6 million, or $0.41 per diluted share, and $16.6 million, or $0.26 per diluted share, respectively.

Revenues for the nine months ended June 30, 2011 were $557.2 million, a 35.5% increase over revenues of $411.3 million for the nine months ended June 30, 2010. Net income attributable to Brooks for the nine months ended June 30, 2011 was $116.3 million or $1.79 per diluted share, as compared to $34.8 million or $0.54 per diluted share for the nine months ended June 30, 2010. Excluding the impact of special charges and non-recurring income, net income increased to $73.9 million or $1.14 per diluted share for the nine months ended June 30, 2011 as compared to $25.9 million or $0.40 per diluted share, for the nine months ended June 30, 2010.

— more —

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

Brooks Automation Reports Third Quarter Financial Results page two

Adjusted Earnings before Interest, Tax, Depreciation and Amortization for the third quarter of fiscal 2011 was $29.5 million, which compared to $34.1 million in the second quarter of fiscal 2011 and $22.5 million in the third quarter of fiscal 2010. 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 included in this release. Adjusted Earnings before Interest, Tax, Deprecation and Amortization for the nine months ended June 30, 2011 was $93.5 million as compared to $45.4 million for the nine months ended June 30, 2010.

Net cash provided by operating activities for the third quarter of fiscal 2011 was $28.3 million, which together with net proceeds from the company’s M&A activities of $76.7 million and net of capital expenditures of $1.0 million resulted in an increase of total cash and marketable securities to $282.4 million at June 30, 2011. For the first nine months of the fiscal year cash from operating activities was $67.2 million and the increase in total cash and marketable securities was $139.9 million.

Steve Schwartz, Chief Executive Officer and President of Brooks stated, “We have seen a high level of uncertainty associated with our near-term revenues into semiconductor markets with significant demand adjustments from our OEM customers consistent with the public outlook they have provided. This trend had been generally negative, however our positioning into adjacent markets is cushioning Brooks from the worst of this current demand correction.”

Dr. Schwartz continued, “In the coming months we will have significant focus on the successful integration of our Nexus Biosystems and RTS Life Sciences acquisitions. The formation of Brooks Life Science Systems is intended to be a vehicle for substantial long term growth in the Life Sciences market of which our initial growth in Biobanking and Automated Sample Management Systems will be a key foundation.”

The Company additionally announced that the Board of Directors had declared a dividend of $0.08 per share payable on September 30, 2011 to stock holders of record on September 9, 2011. Future dividend declarations, as well as the record and payment dates for such dividends, are subject to the final determination of the Company’s Board of Directors.

Martin Headley, Executive Vice-President and Chief Financial Officer, observed that “The initiation of a dividend payment represents a third leg to enhancing shareholder value following the focus on higher performing components in our core business and the start of investment in a new growth platform through recent acquisitions.”

— more —

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

Brooks Automation Reports Third Quarter Financial Results page three

Brooks management will webcast its third quarter earnings conference 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.

# # #

About Brooks Automation, Inc.

Brooks is a leading worldwide provider of automation, vacuum and instrumentation solutions to markets where our technologies provide superior value in controlled environments; our engineering competencies provide our customers with speed to market; and our global service capabilities ensure rapid uptime response. Global semiconductor manufacturing is our heritage and the largest market we currently serve. However, through our product initiatives and business acquisitions, we are increasingly meeting the needs of customers across a broad spectrum of applications in life sciences, analytical & research markets, and clean energy solutions. For more information go to www.brooks.com.

“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 revenue and operating margin expectations, our ability to develop further our business in new and adjacent markets, 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 demand for our products due to difficulties in obtaining components and materials from our suppliers - particularly those manufacturing in Japan — 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; price competition; disputes concerning intellectual property; continuing uncertainties in global political and economic conditions, 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. t 15 Elizabeth Drive t Chelmsford, Massachusetts 01824 t (978)262-2400 t www.brooks.com

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

	June 30,			September 30,
	2011			2010
Assets
Current assets
Cash and cash equivalents	$	133,115		$	59,823
Restricted cash		760			—
Marketable securities		64,804			49,011
Accounts receivable, net		82,547			92,273
Inventories, net		93,525			115,787
Prepaid expenses and other current assets		10,179			10,437
Total current assets		384,930			327,331
Property, plant and equipment, net		58,270			63,669
Long-term marketable securities		83,686			33,593
Goodwill		51,694			48,138
Intangible assets, net		10,395			11,123
Equity investment in joint ventures		34,747			31,746
Other assets		2,637			2,624
Total assets	$	626,359		$	518,224
Liabilities and equity
Current liabilities
Accounts payable	$	45,177		$	65,734
Deferred revenue		7,640			4,365
Accrued warranty and retrofit costs		7,617			8,195
Accrued compensation and benefits		15,449			13,677
Accrued restructuring costs		566			3,509
Accrued income taxes payable		3,930			1,040
Accrued expenses and other current liabilities		9,777			11,635
Total current liabilities		90,156			108,155
Income taxes payable		13,223			12,446
Long-term pension liability		5,728			5,466
Other long-term liabilities		3,280			2,805
Total liabilities		112,387			128,872
Contingencies
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, 79,521,639 shares issued and 66,059,770 shares outstanding at June 30, 2011, 78,869,331 shares issued and 65,407,462 shares outstanding at September 30, 2010		795			789
Additional paid-in capital		1,807,102			1,803,121
Accumulated other comprehensive income		23,865			19,510
Treasury stock at cost, 13,461,869 shares at June 30, 2011 and September 30, 2010		(200,956	)		(200,956	)
Accumulated deficit		(1,117,395	)		(1,233,649	)
Total Brooks Automation, Inc. stockholders’ equity		513,411			388,815
Noncontrolling interest in subsidiaries		561			537
Total equity		513,972			389,352
Total liabilities and equity	$	626,359		$	518,224

Brooks Automation, Inc. t 15 Elizabeth Drive t Chelmsford, Massachusetts 01824 t (978)262-2400 t 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,
	2011			2010			2011			2010
Revenues
Product	$	166,658		$	141,681		$	502,783		$	366,467
Services		19,478			15,109			54,371			44,873
Total revenues		186,136			156,790			557,154			411,340
Cost of revenues
Product		115,299			99,086			342,933			263,556
Services		13,867			11,799			38,258			36,683
Total cost of revenues		129,166			110,885			381,191			300,239
Gross profit		56,970			45,905			175,963			111,101
Operating expenses
Research and development		10,025			7,901			28,365			23,119
Selling, general and administrative		24,676			21,200			74,399			61,021
Restructuring charges		97			288			557			2,294
Total operating expenses		34,798			29,389			103,321			86,434
Operating income		22,172			16,516			72,642			24,667
Interest income		350			221			886			814
Interest expense		10			7			39			34
Sale of intellectual property rights		—			—			—			7,840
Sale of contract manufacturing business		45,009			—			45,009			—
Loss on investment		—			—			—			191
Other (income) expense, net		(1,068	)		7			(1,485	)		295
Income before income taxes and equity in earnings (losses) of joint ventures		68,589			16,723			119,983			32,801
Income tax provision (benefit)		3,300			(35	)		5,323			(2,219	)
Income before equity in earnings (losses) of joint ventures		65,289			16,758			114,660			35,020
Equity in earnings (losses) of joint ventures		900			(112	)		1,618			(303	)
Net income	$	66,189		$	16,646		$	116,278		$	34,717
Add: Net loss (income) attributable to noncontrolling interests		(6	)		(74	)		(24	)		89
Net income attributable to Brooks Automation, Inc.	$	66,183		$	16,572		$	116,254		$	34,806
Basic net income per share attributable to Brooks Automation, Inc. common stockholders	$	1.02		$	0.26		$	1.80		$	0.55
Diluted net income per share attributable to Brooks Automation, Inc. common stockholders	$	1.02		$	0.26		$	1.79		$	0.54
Shares used in computing earnings per share
Basic		64,668			63,969			64,481			63,679
Diluted		65,141			64,264			64,941			64,123

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

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

	Nine months ended
	June 30,
	2011			2010
Cash flows from operating activities
Net income	$	116,278		$	34,717
Adjustments to reconcile net income to net cash provided by operating activities:
Depreciation and amortization		12,336			14,029
Sale of intellectual property rights		—			(7,840	)
Stock-based compensation		5,211			4,889
Amortization of premium on marketable securities		1,534			626
Undistributed (earnings) losses of joint ventures		(1,618	)		303
(Gain) loss on disposal of long-lived assets		24			(4	)
Sale of contract manufacturing business		(45,009	)		—
Loss on investment		—			191
Changes in operating assets and liabilities, net of acquisitions and disposals:
Accounts receivable		(461	)		(33,946	)
Inventories		(11,248	)		(33,683	)
Prepaid expenses and other current assets		3,245			(3,065	)
Accounts payable		(11,812	)		44,256
Deferred revenue		(1,410	)		1,598
Accrued warranty and retrofit costs		(638	)		1,769
Accrued compensation and benefits		(72	)		(2,433	)
Accrued restructuring costs		(2,943	)		(3,043	)
Accrued expenses and other		3,802			(482	)
Net cash provided by operating activities		67,219			17,882
Cash flows from investing activities
Purchases of property, plant and equipment		(4,163	)		(1,908	)
Purchases of marketable securities		(145,821	)		(95,722	)
Sale/maturity of marketable securities		78,644			67,492
Increase in restricted cash		(760	)		—
Proceeds from the sale of the contract manufacturing business		75,664			—
Proceeds from assets sold		4,372			—
Acquisition of RTS Life Sciences, net of cash acquired		(3,381	)		—
Proceeds from the sale of intellectual property rights		—			7,840
Purchase of intangible assets		—			(892	)
Other		—			243
Net cash provided by (used in) investing activities		4,555			(22,947	)
Cash flows from financing activities
Proceeds from issuance of common stock, net of issuance costs		681			609
Net cash provided by financing activities		681			609
Effects of exchange rate changes on cash and cash equivalents		837			(542	)
Net increase (decrease) in cash and cash equivalents		73,292			(4,998	)
Cash and cash equivalents, beginning of period		59,823			59,985
Cash and cash equivalents, end of period	$	133,115		$	54,987

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

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 non-recurring income and special charges such as restructuring charges 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 and diluted earnings per share from operations is presented below:

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

	Quarter ended
	June 30, 2011						March 31, 2011				June 30, 2010
	$			per share			$		per share		$		per share
Net income attributable to Brooks Automation, Inc.	$	66,183		$	1.02		$	26,585	$	0.41	$	16,572	$	0.26
Purchase accounting impact on contracts acquired		313			0.00			—		—		—		—
Restructuring charges		97			0.00			246		0.00		288		0.00
Gain on sale of contract manufacturing, net of tax		(42,588	)		(0.65	)		—		—		—		—
Litigation settlement		(664	)		(0.01	)		—		—		—		—
Adjusted net income attributable to Brooks Automation, Inc.		23,341			0.36			26,831		0.41		16,860		0.26
Stock-based compensation		1,595			0.02			2,407		0.04		1,328		0.02
Adjusted net income attributable to Brooks Automation, Inc. — excluding stock- based compensation	$	24,936		$	0.38		$	29,238	$	0.45	$	18,188	$	0.28

	Nine Months Ended
	June 30, 2011						June 30, 2010
	$			per share			$			per share
Net income attributable to Brooks Automation, Inc.	$	116,254		$	1.79		$	34,806		$	0.54
Purchase accounting impact on contracts acquired		313			0.00			—			—
Restructuring charges		557			0.01			2,294			0.04
Gain on sale of contract manufacturing, net of tax		(42,588	)		(0.66	)		—			—
Litigation settlement		(664	)		(0.01	)		—			—
Sale of intellectual property rights, net of tax		—			—			(7,519	)		(0.12	)
Loss on investment		—			—			191			0.00
One-time income tax benefit		—			—			(3,899	)		(0.06	)
Adjusted net income attributable to Brooks Automation, Inc.	$	73,872			1.14		$	25,873			0.40
Stock-based compensation		5,211			0.08			4,889			0.08
Adjusted net income attributable to Brooks Automation, Inc. — excluding stock- based compensation	$	79,083		$	1.22		$	30,762		$	0.48

	Quarter ended									Nine months ended
	June 30,			Mar 31,			June 30,			June 30,			June 30,
	2011			2011			2010			2011			2010
Net income attributable to Brooks Automation, Inc.	$	66,183		$	26,585		$	16,572			116,254			34,806
Less: Interest income		(350	)		(261	)		(221	)		(886	)		(814	)
Add: Interest expense		10			28			7			39			34
Add: Income tax provision (benefit)		3,300			1,035			(35	)		5,323			(2,219	)
Add: Depreciation		2,990			3,109			3,597			9,444			11,144
Add: Amortization of completed technology		539			480			479			1,498			1,408
Add: Amortization of acquired intangible assets		495			449			493			1,394			1,477
Add: Stock-based compensation		1,595			2,407			1,328			5,211			4,889
Add: Restructuring charges		97			246			288			557			2,294
Add: Loss on investment		—			—			—			—			191
Add: Purchase accounting impact on contracts acquired								313			313			—
Less: Gain on sale of contract manufacturing, pre-tax								(45,009	)		(45,009	)		—
Less: Litigation settlement											(664	)		(664	)
Less: Sale of intellectual property rights, pre-tax		—			—			—			—			(7,840	)
Adjusted EBITDA	$	29,499		$	34,078		$	22,508		$	93,474		$	45,370

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

EX-99.2

Exhibit 99.2

(c) Copyright 2011 by Brooks Automation, Inc. - Proprietary Information 1 3rd Quarter Fiscal 2011 Financial Results Conference Call August 4, 2011

(c) Copyright 2011 by Brooks Automation, Inc. - Proprietary Information 2 Safe Harbor Statement "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 9/30/10. The Company assumes no obligation to update the information in this presentation. Regulation G This presentation contains certain non-GAAP measures which are provided to assist in an understanding of the Brooks business and it's operational performance. These measures should always be considered in conjunction with the appropriate GAAP measure. Reconciliations of all non-GAAP amounts to the relevant GAAP amount are provided in either an attachment to our first quarter financial results press release issued on August 4, 2011 or as an attachment to call slides used to accompany prepared comments made during our financial results conference call of the same date. Both documents are available on our web site at www.brooks.com.

Targeted market Biobanking and Automated Sample Management Key characteristics: automation in a controlled cold environment with abilities to track individual samples and sample characteristics Sample management cycle includes sample preparation and delivery to sample test environment 25 - 30% CAGR for samples under storage Prior growth driven by drug compound storage demands from large pharmaceutical companies and national blood sample initiatives such as the UK Bio Bank Acceleration of growth rate anticipated with increased personalized medicine Automated store development will also benefit from the need to move from manual stores to automated stores to meet volume and sample integrity requirements Brooks Life Science Systems

Nexus Biosystems A leader in the minus 80o C market Significant consumables business for sample plates, micro sample plates and tubes (REMP and Aurora brand names well respected) Nexus and RTS together form Brooks Life Science Systems Brooks Life Science Systems has 45% of installed automated sample stores Installed base capacity to manage 325 million samples Trailing twelve month revenues for RTS and Nexus in the life sciences market approximately $48 million Next actions include rationalization of supporting infrastructure Will enhance R&D activities including commitment of Brooks resources Life Science Systems expected to be accretive to fiscal 2012 Brooks Life Science Systems

(c) Copyright 2011 by Brooks Automation, Inc. - Proprietary Information 5 Significant Events Reflected in June Quarter Financials First Life Science Systems acquisition April 1 - included for full quarter within the Brooks Product Solutions results. Contract manufacturing business sold June 28 - included as a separate segment under the restructured management responsibilities. After tax gain on sale of $42.6 million Reflecting management changes in Products and Systems group we have combined reporting under new division title - Brooks Product Solutions Service organization reset includes renaming - Brooks Global Services. This organization also takes responsibility for all after service support including end-user spares. Settlement of Section 16 shareholder lawsuit by a former CEO leads to gain of $0.6 million

(c) Copyright 2011 by Brooks Automation, Inc. - Proprietary Information 6 Revenue and Earnings Waterfall 2nd Quarter Fiscal 2011 $ 192.7 $27.0 Contract manufacturing ( 6.8) ( 2.3) Acquisition 2.2 0.0 Other Product volume and mix ( 2.7) ( 1.9) Product Warranty ( 0.8) Brooks Global Services 0.7 0.5 Increased investment in engineering ( 0.6) Reduced stock compensation and other variable compensation expense 0.7 3rd Quarter Fiscal 2011 $ 186.1 $22.6 Revenues Operating Profit before Special Charges $ millions

(c) Copyright 2011 by Brooks Automation, Inc. - Proprietary Information 7 Operating Margin impacted by Overhead Absorption and Product Mix $ millions Q2FY11 Q3FY11 Change Revenues $ 192.7 $ 186.1 $ ( 6.6) Gross Profit, (excluding acquisition accounting)* 61.7 57.3 (4.4) Gross Margin % 32.0% 30.8% - 1.2% Research & development 9.5 10.0 (0.5) Selling, general & administrative 25.2 24.7 0.5 Operating Income (before special charges)* $ 27.0 $ 22.6 $ (4.4) * Non -GAAP measure See www.brooks.com for reconciliation to the appropriate GAAP measure

(c) Copyright 2011 by Brooks Automation, Inc. - Proprietary Information 8 Significant Impact of Non-recurring Income $ millions Q2FY11 Q3FY11 Change Revenues $ 192.7 $ 186.1 $( 6.6) Operating profit (before special charges)* 27.0 22.6 ( 4.4) Special charges* (0.2) (0.4) ( 0.2) After-tax gain on sale of business* 0.0 42.6 42.6 Other items 0.4 1.4 1.0 Income taxes, excl gain on sale* (1.0) (0.9) 0.1 Minorities & joint venture earnings 0.4 0.9 0.5 Net Income Attributable to Brooks $ 26.6 $ 66.2 $ 39.6 GAAP DEPS $ 0.41 $ 1.02 $ 0.61 Adjusted DEPS * $ 0.41 $ 0.36 $(0.05) * Non -GAAP measure See www.brooks.com for reconciliation to the appropriate GAAP measure

(c) Copyright 2011 by Brooks Automation, Inc. - Proprietary Information 9 Cash flow Components Adjusted EBITDA * $ 29.5 Restructuring Cash Flow ( 1.1) Reduction in accounts receivable 6.6 Other working capital ( 6.7) Capital expenditures ( 1.0) M & A activity, net 76.7 Net Change in Cash and Marketable securities $ 103.9 FY11 Q3 $ millions * Non -GAAP measure See www.brooks.com for reconciliation to the appropriate GAAP measure

(c) Copyright 2011 by Brooks Automation, Inc. - Proprietary Information 10 Selected Balance Sheet Accounts Cash & marketable securities 178.5 282.4 Accounts Receivable, net 99.6 82.5 DSO at 52 days adjusting for divestiture Inventories, net 126.6 93.5 Divestiture of Contract Manufacturing business Accounts Payable ( 61.0) ( 45.0) Divestiture of Contract Manufacturing business Accrued compensation ( 12.9) ( 15.4) Payroll cycle timing FY11 Q2 FY11 Q3 $ millions

(c) Copyright 2011 by Brooks Automation, Inc. - Proprietary Information 11 Return on Invested Capital Net Income 26.6 66.2 Less: Special charges, non-recurring income and interest income 0.0 (43.2) Operating Return 26.6 23.0 Shareholders Equity 444.4 514.0 Less: Cash & Marketable Securities 178.5 282.4 Investment in Operations 265.9 231.6 Annualized Return on Invested Capital 40.0% 39.7% Q2 FY11 Q3 FY11 $ millions

(c) Copyright 2011 by Brooks Automation, Inc. - Proprietary Information 12 Brooks Product Solutions $ millions Q2FY11 Q3FY11 Comments on Sequential Trends Revenues $ 121.7 $ 121.3 Semi and data storage end market declines Gross Profit 47.5 45.1 Margin 37.2%, includes intangibles amortization of $0.4 in Q2 and $0.5 in Q3 Operating Expenses 26.8 27.6 RTS infrastructure costs and increased engineering Segment Operating Income $ 20.7 $ 17.5 14.5% operating margin

(c) Copyright 2011 by Brooks Automation, Inc. - Proprietary Information 13 Brooks Global Services $ millions Q2FY11 Q3FY11 Comments on Sequential Trends Revenues $ 21.9 $ 22.6 Double digit pump service growth Gross Profit 7.9 7.9 Gross margin 35.0% Operating Expenses 4.8 4.4 Less corporate allocations Segment Operating Income $ 3.1 $ 3.5 Operating margin 15.6%

(c) Copyright 2011 by Brooks Automation, Inc. - Proprietary Information 14 Revenue Guidance $ millions Q3FY11 Q4FY11 Comments on Sequential Trends Core business 141.6 125.0 - 133.0 WFE down 18% - 24% Other served markets show flat to modest increase Contract manufacturing 42.3 0.0 Sold June 28, 2011 Acquisitions 2.2 6.0 - 8.0 Acquisition accounting could diminish recognized revenues GAAP Revenues 186.1 132.0 - 140.0

(c) Copyright 2011 by Brooks Automation, Inc. - Proprietary Information 15 Margin & Earnings Guidance $ millions Q3FY11 Q4FY11 Comments on Sequential Trends Revenues $ 186.1 $132.0 - $140.0 Gross margins 31% 36 - 37% Pro-forma margins for Q3FY11 36.4% Operating Expenses $ 34.7 $ 32.0 - 37.0 Operating expenses of acquired business exceed expense of divested business. Adjusted DEPS * $ 0.36 $ 0.24 - $0.30 * Non -GAAP measure. See www.brooks.com for reconciliation of historical measure to GAAP measure

(c) Copyright 2011 by Brooks Automation, Inc. - Proprietary Information 16 3rd Quarter Fiscal 2011 Financial Results Conference Call August 4, 2011

GAAP to Non-GAAP Reconciliation GAAP non-GAAP GAAP non-GAAP in millions Q2 FY11 Adjust Q2 FY11 Q3 FY11 Adjust Q3 FY11 Revenues $ 192.7 $ - $ 192.7 $ 186.1 $ - $ 186.1 Cost of revenues 131.0 - 131.0 129.1 (0.3) 128.8 Gross profit 61.7 - 61.7 57.0 0.3 57.3 Operating expense: Research & development 9.5 - 9.5 10.0 - 10.0 Selling, general & administrative 25.2 - 25.2 24.7 - 24.7 Restructuring 0.2 (0.2) - 0.1 (0.1) - 34.9 (0.2) 34.7 34.8 (0.1) 34.7 Operating profit (loss) 26.8 0.2 27.0 22.2 0.4 22.6 Interest income, net 0.2 0.2 0.3 0.3 Sale of contract manufacturing business - - - 45.0 (45.0) - Other, net 0.2 - 0.2 1.1 (0.7) 0.4 Income before taxes, joint ventures and minority interest 27.2 0.2 27.4 68.6 (45.3) 23.3 Income tax provision 1.0 - 1.0 3.3 (2.4) 0.9 Net income before joint ventures and minority interest 26.2 0.2 26.4 65.3 (42.9) 22.4 Joint venture income (losses) 0.4 - 0.4 0.9 - 0.9 Net income 26.6 0.2 26.8 66.2 (42.9) 23.3 Net (income) loss attributable to minority interests (0.0) - (0.0) (0.0) - (0.0) Net income (loss) attributable to Brooks $ 26.6 $ 0.2 $ 26.8 $ 66.2 $ (42.9) $ 23.3 Basic earnings per share attributable to Brooks $ 0.41 $ 0.00 $ 0.41 $ 1.02 $ (0.66) $ 0.36 Diluted earnings per share attributable to Brooks $ 0.41 $ 0.00 $ 0.41 $ 1.02 $ (0.66) $ 0.36 Basic shares for EPS 64,516 64,516 64,516 64,668 64,668 64,668 Diluted shares for EPS 65,061 65,061 65,061 65,141 65,141 65,141 Adjustments Cost of revenues Purchasing accounting adjustments to RTS sales contracts $ (0.3) Operating expense: Restructuring $ (0.2) $ (0.1) Sale of contract manufacturing business $ (45.0) Other, net Litigation settlement $ (0.7) Income tax provision Tax on gain from sale of contract manufacturing business $ (2.4)

Unaudited historical segment data, in thousands: (c) Copyright 2011 by Brooks Automation, Inc. - Proprietary Information 18 i Fiscal Year 2010 - by quarter Fiscal Year 2010 - by quarter Fiscal Year 2010 - by quarter Fiscal Year 2010 - by quarter Fiscal Year 2011 - prior quarters Fiscal Year 2011 - prior quarters Year ended Year ended Year ended Quarter ended Quarter ended Quarter ended Quarter ended Quarter ended Quarter ended Sept. 30, 2008 Sept. 30, 2009 Sept. 30, 2010 Dec. 31, 2009 Mar 31, 2010 June 30, 2010 Sept. 30, 2010 Dec. 31, 2010 Mar 31, 2011 Brooks Product Solutions Revenues 362,778 132,337 362,524 63,189 88,280 97,059 113,996 112,001 121,664 Gross profit 108,566 15,140 128,479 20,279 28,870 36,330 43,000 43,090 47,490 Segment operating income (loss) (48) (70,326) 40,143 248 7,438 14,197 18,260 17,471 20,677 Brooks Global Services Revenues 85,660 59,004 74,905 18,389 18,789 18,128 19,599 20,476 21,864 Gross profit 14,126 6,478 20,354 4,388 5,128 5,025 5,813 7,267 7,920 Segment operating income (loss) (6,939) (10,227) 3,805 618 1,100 1,058 1,029 2,510 3,062 Contract Manufacturing Revenues 77,928 27,365 155,543 24,619 41,284 41,603 48,037 45,890 49,123 Gross profit 4,136 (6,690) 17,462 1,579 4,952 4,550 6,381 6,962 6,264 Segment operating income (loss) (8,762) (16,128) 8,335 (564) 2,753 2,273 3,873 4,643 4,000