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): May 5, 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))

ITEM 2.02 RESULTS OF OPERATIONS AND FINANCIAL CONDITION

On May 5, 2011, Brooks Automation, Inc. (“Brooks” or the “Company”) announced via press release its financial results for the fiscal quarter ended March 31, 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 May 5, 2011 to discuss its financial results for the fiscal quarter ended March 31, 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 May 5, 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 

Vice President, General Counsel and Secretary 

Date: May 5, 2011

EXHIBIT INDEX

Exhibit No.		Description
	99.1	Press release issued on May 5, 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 Second Quarter Financial Results

Chelmsford, Massachusetts May 5, 2011 — Brooks Automation, Inc. (Nasdaq: BRKS) announced financial results for the Company’s second quarter of fiscal year 2011 ended on March 31, 2011.

Revenues for the second quarter of fiscal 2011 were $192.7 million, compared to revenues of $148.4 million in the second quarter of fiscal 2010, an increase of 29.9%. Sequentially, revenues increased 8.0% from first quarter fiscal 2011 revenues of $178.4 million. Order bookings for the second quarter of fiscal 2011 were $193.7 million, a 4.7% increase over order bookings in the fiscal first quarter of $184.9 million.

Net income attributable to Brooks Automation, Inc. (“Brooks”) for the second quarter of fiscal 2011 amounted to $26.6 million, or $0.41 per diluted share.

Excluding special charges or non-recurring income, the adjusted net income of $26.8 million or $0.41 per diluted share compares on a sequential basis with $23.7 million or $0.37 per diluted share and improves from income of $10.1 million or $0.16 per diluted share in the second quarter of fiscal 2010. Special charges and non-recurring income and their impact on comparative results are identified in the unaudited table included with this release. Including special charges and non-recurring income, the Net income attributable to Brooks in the first quarter of fiscal 2011 and the second quarter of fiscal 2011 was $23.5 million or $0.36 per diluted share and $21.0 million or $0.33 per diluted share, respectively.

Revenues for the six months ended March 31, 2011 were $371.0 million, a 45.8% increase over revenues of $254.6 million for the six months ended March 31, 2010. Net income attributable to Brooks for the six months ended March 31, 2011 were $50.1 million or $0.77 per diluted share as compared to $18.2 million or $0.28 per diluted share for the six months ended March 31, 2010. Excluding the impact of special charges and non-recurring income, net income increased to $50.5 million or $0.78 per diluted share for the six months ended March 31, 2011 as compared to $9.0 million or $0.14 per diluted share for the six months ended March 31, 2010.

-- more --

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

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

Adjusted Earnings before Interest, Tax, Depreciation and Amortization for the second quarter of fiscal 2011 rose to $34.1 million, which compared to $29.9 million in the first quarter of fiscal 2011 and $17.3 million in the second 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.

Net cash provided by operating activities for the second quarter of fiscal 2011 was $21.2 million, which net of capital expenditures of $1.5 million and other non-operating cash inflow of $0.9 million resulted in an increase of total cash and marketable securities to $178.5 million at March 31, 2011. For the first six months of the fiscal year cash from operating activities has been $38.9 million and the increase in total cash and marketable securities has been $36.1 million.

Martin S. Headley, Executive Vice-President and Chief Financial Officer observed, “Continued gross margin expansion in our Critical Solutions Group and Global Customer Operations drove our growth in Operating Income and Operating Margins. The tragic circumstances in Japan had a modest negative effect on the quarter’s financial results and have created certain supply chain situations that we are monitoring closely for potential impact on the second half of the fiscal year.”

Mr. Headley added “We are actively working through the various closing conditions required to complete our previously announced transaction to sell our contract manufacturing operations to Celestica LLC. We continue to believe that this transaction will close during the June 2011 fiscal quarter.”

Commenting on recent activities, Stephen S. Schwartz, Chief Executive Officer and President of Brooks stated, “The breadth of our technology engagement in terms of both customer and end market application provides for continuing growth even in a period of leveling demands from some of our larger customers in core wafer front end markets. We also expect to continue expanding gross margins at the same time as we ramp up our investments in innovation.”

Brooks management will web cast its second 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.

# # #

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

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

About Brooks Automation, Inc.

Brooks is a leading worldwide provider of automation, vacuum and instrumentation solutions to the global semiconductor and related industries. Our products and services are meeting the needs of customers across a broad spectrum of applications and industries and the global semiconductor manufacturing sector is our largest served market. When demanding productivity and availability objectives are essential factors for success, customers throughout the world turn to Brooks Automation, Inc. For more information go to www.brooks.com or email sales@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)

	March 31,			September 30,
	2011			2010
Assets
Current assets
Cash and cash equivalents	$	59,328		$	59,823
Restricted cash		3,788			—
Marketable securities		59,540			49,011
Accounts receivable, net		99,646			92,273
Inventories, net		126,615			115,787
Prepaid expenses and other current assets		6,372			10,437
Total current assets		355,289			327,331
Property, plant and equipment, net		60,499			63,669
Long-term marketable securities		55,832			33,593
Goodwill		48,138			48,138
Intangible assets, net		9,265			11,123
Equity investment in joint ventures		33,535			31,746
Other assets		2,725			2,624
Total assets	$	565,283		$	518,224
Liabilities and equity
Current liabilities
Accounts payable	$	61,042		$	65,734
Deferred revenue		4,515			4,365
Accrued warranty and retrofit costs		7,667			8,195
Accrued compensation and benefits		12,919			13,677
Accrued restructuring costs		1,553			3,509
Accrued income taxes payable		1,294			1,040
Accrued expenses and other current liabilities		10,051			11,635
Total current liabilities		99,041			108,155
Income taxes payable		12,974			12,446
Long-term pension liability		5,754			5,466
Other long-term liabilities		3,071			2,805
Total liabilities		120,840			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, 79,612,163 shares issued and 66,150,294 shares outstanding at March 31, 2011, 78,869,331 shares issued and 65,407,462 shares outstanding at September 30, 2010		796			789
Additional paid-in capital		1,805,799			1,803,121
Accumulated other comprehensive income		21,827			19,510
Treasury stock at cost, 13,461,869 shares at March 31, 2011 and September 30, 2010		(200,956	)		(200,956	)
Accumulated deficit		(1,183,578	)		(1,233,649	)
Total Brooks Automation, Inc. stockholders’ equity		443,888			388,815
Noncontrolling interest in subsidiaries		555			537
Total equity		444,443			389,352
Total liabilities and equity	$	565,283		$	518,224

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						Six months ended
	March 31,						March 31,
	2011			2010			2011			2010
Revenues
Product	$	175,211		$	133,389		$	336,635		$	224,910
Services		17,440			14,964			34,383			29,640
Total revenues		192,651			148,353			371,018			254,550
Cost of revenues
Product		118,863			97,271			228,066			164,516
Services		12,114			12,132			23,959			24,838
Total cost of revenues		130,977			109,403			252,025			189,354
Gross profit		61,674			38,950			118,993			65,196
Operating expenses
Research and development		9,442			7,677			18,340			15,218
Selling, general and administrative		25,245			20,842			49,723			39,821
Restructuring charges		246			484			460			2,006
Total operating expenses		34,933			29,003			68,523			57,045
Operating income		26,741			9,947			50,470			8,151
Interest income		261			265			536			593
Interest expense		28			11			29			27
Sale of intellectual property rights		—			7,840			—			7,840
Loss on investment		—			—			—			191
Other (income) expense, net		(256	)		91			(417	)		288
Income before income taxes and equity in earnings (losses) of joint ventures		27,230			17,950			51,394			16,078
Income tax provision (benefit)		1,035			(2,819	)		2,023			(2,184	)
Income before equity in earnings (losses) of joint ventures		26,195			20,769			49,371			18,262
Equity in earnings (losses) of joint ventures		408			179			718			(191	)
Net income	$	26,603		$	20,948		$	50,089		$	18,071
Add: Net loss (income) attributable to noncontrolling interests		(18	)		81			(18	)		163
Net income attributable to Brooks Automation, Inc.	$	26,585		$	21,029		$	50,071		$	18,234
Basic net income per share attributable to Brooks Automation, Inc. common stockholders	$	0.41		$	0.33		$	0.78		$	0.29
Diluted net income per share attributable to Brooks Automation, Inc. common stockholders	$	0.41		$	0.33		$	0.77		$	0.28
Shares used in computing earnings per share
Basic		64,516			63,679			64,388			63,535
Diluted		65,061			64,196			64,801			64,042

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)

	Six months ended
	March 31,
	2011			2010
Cash flows from operating activities
Net income	$	50,089		$	18,071
Adjustments to reconcile net income to net cash provided by operating activities:
Depreciation and amortization		8,312			9,460
Sale of intellectual property rights		—			(7,840	)
Stock-based compensation		3,616			3,561
Amortization of premium on marketable securities		921			368
Undistributed (earnings) losses of joint ventures		(718	)		191
(Gain) loss on disposal of long-lived assets		14			(4	)
Loss on investment		—			191
Changes in operating assets and liabilities, net of acquisitions and disposals:
Accounts receivable		(6,199	)		(29,258	)
Inventories		(9,744	)		(19,653	)
Prepaid expenses and other current assets		2,853			(4,132	)
Accounts payable		(4,807	)		40,424
Deferred revenue		92			1,062
Accrued warranty and retrofit costs		(538	)		1,414
Accrued compensation and benefits		(2,443	)		(2,972	)
Accrued restructuring costs		(1,956	)		(1,857	)
Accrued expenses and other		(574	)		235
Net cash provided by operating activities		38,918			9,261
Cash flows from investing activities
Purchases of property, plant and equipment		(3,175	)		(1,163	)
Purchases of marketable securities		(71,225	)		(70,872	)
Sale/maturity of marketable securities		37,551			43,757
Increase in restricted cash		(3,788	)		—
Proceeds from the sale of intellectual property rights		—			7,840
Purchase of intangible assets		—			(892	)
Other		—			243
Net cash used in investing activities		(40,637	)		(21,087	)
Cash flows from financing activities
Proceeds from issuance of common stock, net of issuance costs		681			590
Net cash provided by financing activities		681			590
Effects of exchange rate changes on cash and cash equivalents		543			(128	)
Net decrease in cash and cash equivalents		(495	)		(11,364	)
Cash and cash equivalents, beginning of period		59,823			59,985
Cash and cash equivalents, end of period	$	59,328		$	48,621

Brooks Automation, Inc. t 15 Elizabeth Drive t Chelmsford, Massachusetts 01824 t (978)262-2400 t 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 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
	March 31, 2011				December 31, 2010				March 31, 2010
	$ per		share		$ per		share		$ per			share
Net income attributable to Brooks Automation, Inc.	$	26,585	$	0.41	$	23,486	$	0.36	$	21,029		$	0.33
Restructuring charges		246		0.00		214		0.00		484			0.01
One-time income tax benefit		—		—		—		—		(3,899	)		(0.06	)
Sale of intellectual property rights, net of tax		—		—		—		—		(7,519	)	$	(0.12	)
Adjusted net income attributable to Brooks Automation, Inc.		26,831		0.41		23,700		0.37		10,095			0.16
Stock-based compensation		2,407		0.04		1,209		0.02		2,044			0.03
Adjusted net income attributable to Brooks Automation, Inc., excluding stock-based compensation	$	29,238	$	0.45	$	24,909	$	0.39	$	12,139		$	0.19

	Six Months Ended
	March 31, 2011				March 31, 2010
	$ per		share		$ per			share
Net income attributable to Brooks Automation, Inc.	$	50,071	$	0.77	$	18,234		$	0.28
Restructuring charges		460		0.01		2,006			0.03
Loss on investment		—		—		191			0.00
One-time income tax benefit		—		—		(3,899	)		(0.06	)
Sale of intellectual property rights, net of tax		—		—		(7,519	)		(0.12	)
Adjusted net income attributable to Brooks Automation, Inc.	$	50,531		0.78	$	9,013			0.14
Stock-based compensation		3,616		0.06		3,561			0.06
Adjusted net income attributable to Brooks Automation, Inc. — excluding stock-based compensation	$	54,147	$	0.84	$	12,574		$	0.20

	Quarter ended									Six months ended
	Mar 31,			Dec 31,			Mar 31,			Mar 31,			Mar 31,
	2011			2010			2010			2011			2010
Net income attributable to Brooks Automation, Inc.	$	26,585		$	23,486		$	21,029			50,071			18,234
Less: Interest income		(261	)		(275	)		(265	)		(536	)		(593	)
Add: Interest expense		28			1			11			29			27
Add: Income tax provision (benefit)		1,035			988			(2,819	)		2,023			(2,184	)
Add: Depreciation		3,109			3,345			3,701			6,454			7,547
Add: Amortization of completed technology		480			479			472			959			929
Add: Amortization of acquired intangible assets		449			450			493			899			984
Add: Stock-based compensation		2,407			1,209			2,044			3,616			3,561
Add: Restructuring charges		246			214			484			460			2,006
Add: Loss on investment		—			—			—			—			191
Sale of intellectual property rights, pre-tax		—			—			(7,840	)		—			(7,840	)
Adjusted EBITDA	$	34,078		$	29,897		$	17,310		$	63,975		$	22,862

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 2nd Quarter Fiscal 2011 Financial Results Conference Call May 5, 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 its 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 second quarter financial results press release issued on May 5, 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.

(c) Copyright 2011 by Brooks Automation, Inc. - Proprietary Information 3 Revenue Gains of 8% $ millions Q1FY11 Q2FY11 Change Revenues $ 178.4 $ 192.7 $ 14.3 Operating profit (before special charges)* 23.9 27.0 3.1 Special charges (0.2) (0.2) 0.0 Interest & other income 0.4 0.4 0.0 Income taxes (1.0) (1.0) 0.0 Minorities & joint venture earnings 0.3 0.4 0.1 Net Income Attributable to Brooks $ 23.5 $ 26.6 $ 3.1 GAAP DEPS $ 0.36 $ 0.41 $ 0.5 Adjusted DEPS * $ 0.37 $ 0.41 $ 0.4 * Non - GAAP measure See www.brooks.com for reconciliation to the appropriate GAAP measure

(c) Copyright 2011 by Brooks Automation, Inc. - Proprietary Information 4 Operating Margin Expands to 14% $ millions Q1FY11 Q2FY11 Change Revenues $ 178.4 $ 192.7 $ 14.3 Gross Profit 57.3 61.7 4.4 Gross Margin % 32.1% 32.0% .1% Research & development 8.9 9.5 (0.6) Selling, general & administrative 24.5 25.2 (0.8) Operating Income (before special charges)* $ 23.9 $ 27.0 $ 3.1 * Non - GAAP measure See www.brooks.com for reconciliation to the appropriate GAAP measure

(c) Copyright 2011 by Brooks Automation, Inc. - Proprietary Information 5 Revenue and Earnings Waterfall 1st Quarter Fiscal 2011 $ 178.4 $23.9 Critical Solutions 7.9 3.7 Systems Solutions 5.9 0.5 GCO (Service) business growth 0.5 0.2 Increased engineering expense ( 0.6) Reduction in overhead spending 0.5 Increased stock compensation expense ( 1.2) 2nd Quarter Fiscal 2011 $ 192.7 $27.0 Revenues Operating Profit before Special Charges $ millions

(c) Copyright 2011 by Brooks Automation, Inc. - Proprietary Information 6 Cumulative Adjusted EBITDA* Growth at 35% of Revenue Growth Q3FY09 Q4 FY09 Q1FY10 Q2FY10 Q3FY10 Q4 FY10 Q1 FY11 Q2FY11 Revenues 43.9 64.1 106.2 148.4 156.8 181.6 178.4 192.7 Adj EBITDA -17.2 -8.7 5.6 17.3 22.5 29.7 29.9 34.1 R E V E N U E S A D J E B I T D A* Contract Manufacturing mix 24 - 26% * Non - GAAP measure See www.brooks.com for the reconciliation to the appropriate GAAP measure

(c) Copyright 2011 by Brooks Automation, Inc. - Proprietary Information 7 Cash Flow Components Adjusted EBITDA * $ 34.1 Restructuring Cash Flow ( 1.2) Growth in accounts receivable ( 12.0) Other working capital 0.3 Capital expenditures ( 1.5) Other 0.9 Net Change in Cash and Marketable securities $ 20.6 FY11 Q2 $ millions * Non - GAAP measure See www.brooks.com for reconciliation to the appropriate GAAP measure

(c) Copyright 2011 by Brooks Automation, Inc. - Proprietary Information 8 Selected Balance Sheet Accounts Cash & marketable securities 157.9 178.5 Accounts Receivable, net 87.6 99.6 DSO at 47 days with strong March revenues Inventories, net 127.1 126.6 Inventory turns improve to 4.1 x Accounts Payable ( 62.3) ( 61.0) Build of product earlier in the quarter Accrued compensation ( 11.8) ( 12.9) Variable compensation accruals FY11 Q1 FY11 Q2 $ millions

(c) Copyright 2011 by Brooks Automation, Inc. - Proprietary Information 9 Return on Invested Capital Net Income 23.5 26.6 Less: Special charges and interest income 0.0 0.0 Operating Return 23.5 26.6 Shareholders Equity 413.9 444.4 Less: Cash & Marketable Securities 157.9 178.5 Investment in Operations 256.0 265.9 Annualized Return on Invested Capital 36.7% 40.0% Q1 FY11 Q2 FY11 $ millions

(c) Copyright 2011 by Brooks Automation, Inc. - Proprietary Information 10 Critical Solutions Segment $ millions Q1FY11 Q2FY11 Comments on Sequential Trends Revenues $ 74.4 $ 82.4 Vacuum products growth Gross Profit 31.0 34.7 Margin expansion to 42.2% Operating Expenses 17.5 18.2 Increase in engineering investments Segment Operating Income $ 13.5 $ 16.5 20.0% operating margin

(c) Copyright 2011 by Brooks Automation, Inc. - Proprietary Information 11 Systems Solutions Segment $ millions Q1FY11 Q2FY11 Comments on Sequential Trends Revenues $ 86.2 $ 92.1 Principally growth in contract manufacturing Gross Profit 20.6 21.1 Mix of contract manufacturing operations Operating Expenses 10.7 11.2 Segment Operating Income $ 9.9 $ 9.9 10.7% operating margin

(c) Copyright 2011 by Brooks Automation, Inc. - Proprietary Information 12 Global Customer Operations $ millions Q1FY11 Q2FY11 Comments on Sequential Trends Revenues $ 17.7 $ 18.2 Double digit robot service growth Gross Profit 5.7 5.9 Margin expands to 32.4% Operating Expenses 4.4 4.5 Segment Operating Income $ 1.3 $ 1.4 7.7% operating margin

Brooks Life Science Systems RTS revenue annual run rate expectations $ 10 - 12 million Dilution in FY11 < $0.01 Purchase price, net of cash on hand $ 3.3 million

(c) Copyright 2011 by Brooks Automation, Inc. - Proprietary Information 14 Revenue Guidance $ millions Q2FY11 Q3FY11 Comments on Sequential Trends Core business 144.3 138.0 - 145.0 Continuing technology wins across a broad spectrum of OEM's. Strong backlog into the quarter. Contract Manufacturing 48.4 25.0 - 50.0 Driven by timing of the close of sale to Celestica. Life Science Systems 0.0 2.0 - 3.0 Acquired April 1 GAAP Revenues 192.7 165.0 - 195.0

(c) Copyright 2011 by Brooks Automation, Inc. - Proprietary Information 15 Margin & Earnings Guidance $ millions Q2FY11 Q3FY11 Comments on Sequential Trends Revenues $ 192.7 $165.0 - $195.0 Gross margins 32% 31 - 35% Timing of contract manufacturing business sale. Operating Expenses $ 34.7 $ 33.5 - 35.0 Continued engineering build. G&A reductions. Adjusted DEPS * $ 0.41 $ 0.35 - $0.40 * 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 2nd Quarter Fiscal 2011 Financial Results Conference Call May 5, 2011

GAAP to Non-GAAP Reconciliation