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): February 9, 2012 (February 8, 2012)

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:

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

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

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

¨ 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 February 9, 2012, Brooks Automation, Inc. (“Brooks” or the “Company”) announced via press release its financial results for the fiscal quarter ended December 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 February 9, 2012 to discuss its financial results for the fiscal quarter ended December 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 5.07 Submission of Matters to a Vote of Security Holders

The Annual Meeting of the stockholders of Brooks Automation, Inc. (the “Company”) was held on February 8, 2012. The stockholders elected each of the Company’s nominees for director, approved an amendment to the Company’s 1995 Employee Stock Purchase Plan, approved, on an advisory basis the overall compensation of the Company’s executive officers, recommended, on an advisory basis, a frequency of once every year for advisory votes on executive compensation, and ratified the appointment of PricewaterhouseCoopers LLP as the Company’s independent registered accounting firm for the 2012 fiscal year. The proposals below are described in detail in the Company’s definitive proxy statement dated December 23, 2011. The results are as follows:

1. Election of Directors

	For		Withhold		Broker Non-Votes
A. Clinton Allen		51,376,970		584,377		5,040,578
Joseph R. Martin		50,330,270		1,631,077		5,040,578
John K. McGillicuddy		50,039,892		1,921,455		5,040,578
Krishna G. Palepu		51,327,787		633,560		5,040,578
C.S. Park		51,320,769		640,578		5,040,578
Kirk P. Pond		51,160,485		800,862		5,040,578
Stephen S. Schwartz		51,357,434		603,913		5,040,578
Alfred Woollacott, III		51,254,973		706,374		5,040,578
Mark S. Wrighton		51,576,033		385,314		5,040,578

2. Approval of Amendment to Company’s 1995 Employee Stock Purchase Place to increase the number of shares available for issuance thereunder by 1,000,000 shares, from 3,000,000 to 4,000,000

For	Against	Abstain	Broker Non-Votes
51,311,041	456,657	193,649	5,040,578

3. Approval, on an advisory basis, of the overall compensation of the Company’s executive officers

For	Against	Abstain	Broker Non-Votes
50,816,768	1,085,567	59,012	5,040,578

4. Recommendation, on an advisory basis, of the frequency of advisory votes on executive compensation

1 Year	2 Years	3 Years	Abstain	Broker Non-Votes
46,333,652	142,215	5,426,168	59,312	5,040,578

5. Ratification of the selection of PricewaterhouseCoopers LLP

For	Against	Abstain	Broker Non-Votes
52,952,338	3,915,135	134,452	—

Based on these results, and consistent with the recommendation of the Company’s Board of Directors, the Company intends to hold an advisory vote on executive compensation annually until the next required non-binding advisory vote on the frequency of future votes regarding executive compensation.

Item 9.01 Financial Statements and Exhibits

(d) Exhibits

99.1	Press release issued on February 9, 2012 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: February 9, 2012

EXHIBIT INDEX

Exhibit No.	Description
99.1	Press release issued on February 9, 2012 by Brooks Automation, Inc.
99.2	Investor Conference Call Slide Presentation.

EX-99.1

Exhibit 99.1

Brooks Automation Reports Fiscal First Quarter Ended December 31, 2011 Results

CHELMSFORD, Mass., Feb. 9, 2012 (GLOBE NEWSWIRE) — Brooks Automation, Inc. (Nasdaq:BRKS), a leading worldwide provider of automation, vacuum and instrumentation solutions for multiple markets including semiconductor manufacturing, life sciences, and clean energy, today reported preliminary financial results for the first quarter ended December 31, 2011.

Fiscal First Quarter of 2012 Financial and Operational Highlights:

• Revenues were $120.2 Million; Order Bookings increased 16.5% sequentially to $128.5 million;

• GAAP EPS was $0.05 and EPS excluding special charges was $0.06;

• Adjusted EBITDA was $10.8 million;

• Cash, Cash Equivalents and Marketable Securities as of December 31^st were $194.5 million, or $2.98 per diluted share with no Debt;

• Generated 22 Design-in-Wins with OEM Customers, forging Continued Market Share Gains.

Management Comments

“After a slow start to the quarter our semiconductor equipment business recovered later in the quarter resulting in revenues and earnings at the high end of our guidance. We see this momentum accelerating in the March quarter and expect it to be a significant driver behind improving results. We are very pleased with the controllable aspects of our overall financial and operational performance during the first quarter including our integration of the Life Science Systems business which is moving ahead in-line with our expectations,” stated Steve Schwartz, President & Chief Executive Officer of Brooks. “We grew first quarter Life Science Systems revenue to approximately 10% of overall revenue, and we are excited about a number of new product lines we are introducing to our customers including the new Celigo^® product line acquired at the end of December.”

Dr. Schwartz continued, “With our strong cash position, no debt and increasing cash flow as the cyclical market recovery continues, we believe that we will continue to be extremely well placed to continue our existing strong levels of reinvestment in the business as well as make prudently focused strategic acquisitions that build on our core competencies.”

First Quarter of Fiscal 2012 Results

Revenues for the first quarter of fiscal 2012 were $120.2 million, compared to revenues of $131.0 million in the fourth quarter of fiscal 2011 and $178.4 million in the first quarter of fiscal 2011, which included $45.9 million from the contract manufacturing business that was sold at the end of the third quarter of 2011. Revenues for the Brooks Global Services segment decreased 7.7% on a sequential basis compared to the fiscal fourth quarter of 2011, and revenues for the Brooks Product Solutions segment declined 13.4% sequentially due to overall industry weakness.

Order bookings for the first quarter of fiscal 2012 grew 16.5% to $128.5 million, compared to order bookings in the fiscal fourth quarter of $110.3 million.

Gross profit margin was 33.6% for the first quarter of fiscal 2012, compared to gross profit margins of 35.9% for the fourth quarter of fiscal 2011 and 32.1% for the first quarter of fiscal 2011. The first quarter of fiscal 2012 margins were impacted by revenue mix, adverse absorption of fixed overhead costs during the cyclical revenue decline and a number of acquisition and integration related expenses related to Brooks Life Science Systems.

Net income for the first quarter of fiscal 2012 amounted to $3.0 million, or $0.05 per diluted share, which includes $784 thousand of special charges primarily associated with the Life Science Systems merger and acquisition activities. Adjusted Net income excluding these special charges was $3.8 million and compares to $12.1 million or $0.19 per diluted share for the fourth quarter of fiscal 2011 and $23.7 million or $0.37 per diluted share in the first quarter of fiscal 2011.

Adjusted EBITDA (Earnings before Interest, Tax, Depreciation and Amortization) for the first quarter of fiscal 2012 was $10.8 million, which compared to $17.7 million in the fourth quarter of fiscal 2011 and $29.9 million in the first quarter of fiscal 2011. 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 first quarter of fiscal 2012 was $5.1 million, which resulted in total cash and marketable securities of $194.5 million at December 31, 2011.

Quarterly Cash Dividend

The Company additionally announced that the Board of Directors had declared a dividend of $0.08 per share payable on March 30, 2012 to stockholders of record on March 9, 2012. 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.

Guidance for Second Fiscal Quarter

The Company announced revenue and earnings guidance for the second quarter of fiscal 2012. Revenues are expected to range between $132 and $140 million and GAAP earnings, including a charge associated with the acquisition of in process research & development, is expected to range between $0.09 and $0.14. Adjusted EPS excluding this charge is expected to be between $0.15 and $0.20 per diluted share.

Conference Call

Brooks management will webcast its first quarter earnings conference today at 4:30 p.m. Eastern Time to discuss the fiscal first quarter 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.

The call will be broadcast live over the Internet hosted at the Investor Relations section of Brooks’ website at www.brooks.com, and will be archived online on this website for convenient on-demand replay. In addition, you may call (800) 688-0796 (US only) or (617) 614-4070 to listen to the live broadcast. The passcode for this telephone access is 633 410 70.

About Brooks Automation, Inc.

Brooks is a leading worldwide provider of automation, vacuum and instrumentation solutions for multiple markets including semiconductor manufacturing, life sciences, and clean energy. Our technologies, engineering competencies and global service capabilities provide customers speed to market, and ensure high uptime and rapid response, which

equate to superior value in their mission-critical controlled environments. Since 1978, we have been a leading partner to the global semiconductor manufacturing market and through product development initiatives and strategic business acquisitions; we have expanded our reach to meet the needs of customers in the life sciences industry, analytical & research markets, and clean energy solutions. Brooks is headquartered in Chelmsford, MA, with direct operations in North America, Europe and Asia. For more information, please visit 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 Thailand - 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.

BROOKS AUTOMATION, INC.

CONSOLIDATED BALANCE SHEETS

(unaudited)

(In thousands, except share and per share data)

	December 31, 2011			September 30, 2011
Assets
Current assets
Cash and cash equivalents	$	49,213		$	58,833
Restricted cash		863			1,293
Marketable securities		79,465			65,695
Accounts receivable, net		73,684			76,701
Inventories, net		102,612			107,654
Prepaid expenses and other current assets		10,467			10,348
Total current assets		316,304			320,524
Property, plant and equipment, net		67,349			68,596
Long-term marketable securities		65,826			81,290
Goodwill		88,440			84,727
Intangible assets, net		45,547			44,314
Equity investment in joint ventures		35,357			34,612
Other assets		2,981			2,557
Total assets	$	621,804		$	636,620
Liabilities and equity
Current liabilities
Accounts payable	$	34,257		$	40,199
Deferred revenue		11,980			14,073
Accrued warranty and retrofit costs		7,293			7,438
Accrued compensation and benefits		13,150			17,288
Accrued restructuring costs		321			293
Accrued income taxes payable		3,387			4,015
Accrued expenses and other current liabilities		14,040			12,433
Total current liabilities		84,428			95,739
Income taxes payable		11,706			11,728
Long-term pension liability		7,239			7,161
Other long-term liabilities		3,677			3,394
Total liabilities		107,050			118,022
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, 79,716,314 shares issued and 66,254,445 shares outstanding at December 31, 2011, 79,737,189 shares issued and 66,275,320 shares outstanding at September 30, 2011		797			797
Additional paid-in capital		1,810,829			1,809,287
Accumulated other comprehensive income		16,273			19,480
Treasury stock at cost, 13,461,869 shares at December 31, 2011 and September 30, 2011		(200,956	)		(200,956	)
Accumulated deficit		(1,112,786	)		(1,110,599	)
Total Brooks Automation, Inc. stockholders’ equity		514,157			518,009
Noncontrolling interest in subsidiaries		597			589
Total equity		514,754			518,598
Total liabilities and equity	$	621,804		$	636,620

BROOKS AUTOMATION, INC.

CONSOLIDATED STATEMENTS OF OPERATIONS

(unaudited)

(In thousands, except per share data)

	Three months ended December 31,
	2011			2010
Revenues
Product	$	97,098		$	161,189
Services		23,130			17,178
Total revenues		120,228			178,367
Cost of revenues
Product		64,289			108,973
Services		15,582			12,075
Total cost of revenues		79,871			121,048
Gross profit		40,357			57,319
Operating expenses
Research and development		11,949			8,898
Selling, general and administrative		26,742			24,478
Restructuring charges		203			214
Total operating expenses		38,894			33,590
Operating income		1,463			23,729
Interest income		279			275
Interest expense		(7	)		(1	)
Other income, net		346			161
Income before income taxes and equity in earnings of joint ventures		2,081			24,164
Income tax provision		300			988
Income before equity in earnings of joint ventures		1,781			23,176
Equity in earnings of joint ventures		1,225			310
Net income	$	3,006		$	23,486
Net income attributable to noncontrolling interests		(8	)		—
Net income attributable to Brooks Automation, Inc.	$	2,998		$	23,486
Basic net income per share attributable to Brooks Automation, Inc. common stockholders	$	0.05		$	0.37
Diluted net income per share attributable to Brooks Automation, Inc. common stockholders	$	0.05		$	0.36
Shares used in computing earnings per share
Basic		64,812			64,263
Diluted		65,309			64,475

BROOKS AUTOMATION, INC.

CONSOLIDATED STATEMENTS OF CASH FLOWS

(unaudited)

(In thousands)

	Three months ended December 31,
	2011			2010
Cash flows from operating activities
Net income	$	3,006		$	23,486
Adjustments to reconcile net income to net cash provided by operating activities:
Depreciation and amortization		5,268			4,274
Stock-based compensation		1,743			1,209
Amortization of premium on marketable securities		654			410
Undistributed earnings of joint ventures		(1,225	)		(310	)
Gain on disposal of long-lived assets		—			(13	)
Changes in operating assets and liabilities, net of acquisitions and disposals:
Accounts receivable		3,935			4,949
Inventories		5,874			(11,289	)
Prepaid expenses and other current assets		(490	)		2,117
Accounts payable		(5,910	)		(3,424	)
Deferred revenue		(2,427	)		(330	)
Accrued warranty and retrofit costs		(152	)		(314	)
Accrued compensation and benefits		(4,270	)		(2,810	)
Accrued restructuring costs		32			(985	)
Accrued expenses and other		(929	)		713
Net cash provided by operating activities		5,109			17,683
Cash flows from investing activities
Purchases of property, plant and equipment		(2,063	)		(1,638	)
Purchases of marketable securities		(23,579	)		(38,704	)
Sale/maturity of marketable securities		24,549			25,225
Acquisition, net of cash acquired		(8,716	)		—
Decrease in restricted cash		430			—
Net cash used in investing activities		(9,379	)		(15,117	)
Cash flows from financing activities
Common stock dividend paid		(5,185	)		—
Net cash used in financing activities		(5,185	)		—
Effects of exchange rate changes on cash and cash equivalents		(165	)		(77	)
Net increase (decrease) in cash and cash equivalents		(9,620	)		2,489
Cash and cash equivalents, beginning of period		58,833			59,823
Cash and cash equivalents, end of period	$	49,213		$	62,312

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 acquisition related charges. 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:

	Quarter ended
	December 31, 2011				September 30, 2011						December 31, 2010
	$		per share		$			per share			$		per share
Net income (loss) attributable to Brooks Automation, Inc.	$	2,998	$	0.05	$	12,098		$	0.19		$	23,486	$	0.36
Purchase accounting impact on contracts acquired		360		0.01		957			0.01			—		—
Restructuring charges		203		0.00		479			0.01			214		0.00
Merger costs		221		0.00		719			0.01			—		—
Inventory charges recorded for acquisitions		—		—		625			0.01			—		—
One-time tax benefit		—		—		(2,758	)		(0.04	)		—		—
Adjusted net income (loss) attributable to Brooks Automation, Inc.		3,782		0.06		12,120			0.19			23,700		0.37
Stock-based compensation		1,734		0.03		1,541			0.02			1,209		0.02
Adjusted net income attributable to Brooks Automation, Inc., excluding stock-based compensation	$	5,516	$	0.08	$	13,661		$	0.21		$	24,909	$	0.39

	Quarter ended
	Dec 31, 2011			Sept 30, 2011			Dec 31, 2010
Net income (loss) attributable to Brooks Automation, Inc.	$	2,998		$	12,098		$	23,486
Less: Interest income		(279	)		(267	)		(275	)
Add: Interest expense		7			26			1
Add: Income tax provision (benefit)		300			(3,369	)		988
Add: Depreciation		3,262			3,177			3,345
Add: Amortization of completed technology		789			718			479
Add; Amortization of acquired intangible assets		1,217			1,018			450
Add: Stock-based compensation		1,743			1,541			1,209
Add: Restructuring charges		203			479			214
Add: Merger costs		221			719			—
Add: Purchase accounting impact on contracts acquired		360			957			—
Add: Inventory charges recorded for acquisitions		—			625			—
Adjusted EBITDA	$	10,821		$	17,722		$	29,897

CONTACT:

Barbara Culhane

Brooks Automation, Inc.

Corporate Marketing Manager

978-262-2400

barbara.culhane@brooks.com

John Mills

Senior Managing Director

ICR, LLC

310-954-1105

john.mills@icrinc.com

EX-99.2

Exhibit 99.2

Exhibit 99.2

1st Quarter Fiscal 2012 Financial Results Conference Call

February 9, 2012

© Copyright 2012 by Brooks Automation, Inc. – Proprietary Information

1

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 9/30/11. 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 February 9, 2012 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.

© Copyright 2012 by Brooks Automation, Inc. – Proprietary Information 2

Significant Events in the December Quarter

Full quarter of Nexus BioSystems acquisition compared to 2 months reflected in September quarter

Balance sheet includes Celigo product line acquisition that closed on December 30, 2011

Significant slow down in Semiconductor activity early in the quarter with a strong rebound in the last few weeks of the quarter

Industrial capital spend reductions with largest declines for Polycold mixed gas cryo chillers

Effective tax rate fluctuating from quarter to quarter

© Copyright 2012 by Brooks Automation, Inc. – Proprietary Information 3

Revenue and Operating Profits Waterfall

Revenues Operating Profit

$ millions before Special Charges

4th Quarter Fiscal 2011 $ 131.0 $ 9.7

Brooks Life Science Systems 4.3 1.6

Brooks Product Solutions ( 13.2) ( 7.4)

Brooks Global Services ( 1.8) ( 1.3)

Amortization increase in SG&A ( 0.2)

1st Quarter Fiscal 2012 $ 120.2 $ 2.3

© Copyright 2012 by Brooks Automation, Inc. – Proprietary Information 4

Fixed Cost Absorption and Mix Impact Margins

$ millions Q4FY11 Q1FY12 Change

Revenues $ 131.0 $ 120.2 $ ( 10.8)

Gross Profit, (excluding acquisition accounting)* 48.6 40.7 (7.9)

Gross Margin % 37.1% 33.9%—3.2%

Research & development 11.5 11.9 (0.4)

Selling, general & administrative 27.4 26.5 0.9

Operating Income (before special charges)* $ 9.7 $ 2.3 $ (7.4)

* Non –GAAP measure See www.brooks.com for reconciliation to the appropriate GAAP measure

© Copyright 2012 by Brooks Automation, Inc. – Proprietary Information 5

Income Taxes impact Special Charges

$ millions Q4FY11 Q1FY12 Change

Revenues $ 131.0 $ 120.2 $ ( 10.8)

Operating profit (before special charges)* 9.7 2.3 ( 7.4)

Special charges* 0.0 ( 0.8) ( 0.8)

Other items 0.7 0.6 ( 0.1)

Income tax benefit (provision), 0.6 ( 0.3) ( 0.9)

excluding non-recurring items*

Minorities & joint venture earnings 1.1 1.2 0.1

Net Income Attributable to Brooks $ 12.1 $ 3.0 $ (9.1)

GAAP DEPS $ 0.19 $ 0.05 $(0.14)

Adjusted DEPS * $ 0.19 $ 0.06 $(0.13)

* Non –GAAP measure See www.brooks.com for reconciliation to the appropriate GAAP measure

© Copyright 2012 by Brooks Automation, Inc. – Proprietary Information 6

Cash and Cash flow

$ millions FY12 Q1

Adjusted EBITDA * $ 10.8

Working Capital movements (4.3)

Restructuring & undistributed joint venture earnings ( 1.4)

Cash Flow from Operations 5.1 Capital expenditures ( 2.1) Dividends ( 5.2) Celigo acquisition ( 8.7) Other ( 0.4)

Net Change in Cash and Marketable securities ( 11.3)

Cash and Marketable securities at December 31 $ 194.5

* Non –GAAP measure See www.brooks.com for reconciliation to the appropriate GAAP measure

© Copyright 2012 by Brooks Automation, Inc. – Proprietary Information 7

Diversification and Dilution of Customer Exposures

FY11 Q1 FY12 Q1

# of >10% Customers 2 1

% of Business to Top

47% 25%

3 Customers

9% 11%

11% 51%

18%

FY12Q1

Semi front end products

BGS

Industrial

Life Sciences

Other adjacencies

© Copyright 2012 by Brooks Automation, Inc. – Proprietary Information 8

Brooks Life Science Systems

Reconciliation of GAAP to underlying performance

Q1FY12 Adjust- Q1FY12

$ millions Comments

GAAP ments Non-GAAP

Adjustment for fair value

Revenues $ 12.8 $ 0.5 $ 13.3 accounting on contracts

acquired

Gross Profit 4.8 0.4 5.2 39% underlying gross margin

Increased R&D with

Operating 5.5 0.0 5.5 integration savings offsetting

Expenses full quarter effect for SG&A

Segment $( 0.6) $( 0.3)

Operating Loss

© Copyright 2012 by Brooks Automation, Inc. – Proprietary Information 9

Brooks Product Solutions Sequential Performance

Comments on

$ millions Q4FY11 Q1FY12

Sequential Trends

Industrial product revenues

Revenues $ 98.5 $ 85.3 down $10 million

Margin of 33.3% impacted by

Gross Profit 36.7 28.4 absorption and mix

Operating Expenses 28.7 27.3

Segment Operating

Income $ 8.0 $ 1.1 1.3% operating margin

© Copyright 2012 by Brooks Automation, Inc. – Proprietary Information 10

Brooks Global Services Sequential Performance

Comments on $ millions Q4FY11 Q1FY12 Sequential Trends

Revenues $ 23.9 $ 22.1 Decline in spare part demand

Spares mix and favorable Gross Profit 8.7 7.1 materials cost in Sept quarter

Operating Expenses 4.5 4.2

Segment Operating $ 4.2 $ 2.9 13.3% operating margin Income

© Copyright 2012 by Brooks Automation, Inc. – Proprietary Information 11

Revenue, Margin & Earnings Guidance

$ millions Q1FY11 Q2FY12 Comments on Sequential Trends

Front End Semiconductor equipment

recovery. Continued growth in Life

Revenues $ 120.2 $132.0—$140.0 Science Systems business.

$3.5 million reduction in expenses

Adjusted Diluted from recovery of previously expensed

$ 0.06 $ 0.15—$0.20

Earnings Per Share* legal costs and $1.2 million income

tax benefit

$3.0 million in-process R&D charge

GAAP Diluted from IP acquisition. Small

$ 0.05 $ 0.09—$0.14

Earnings Per Share acquisition accounting adjustments

for Life Science Systems

* Non –GAAP measure. See www.brooks.com for reconciliation of historical measure to GAAP measure

© Copyright 2012 by Brooks Automation, Inc. – Proprietary Information 12

1st Quarter Fiscal 2012 Financial Results Conference Call

February 9, 2012

© Copyright 2012 by Brooks Automation, Inc. – Proprietary Information 13

GAAP to Non-GAAP Reconciliation – Q4 FY11 vs. Q1 FY12

GAAP non-GAAP GAAP non-GAAP

in millions Q4 FY11 Adjust Q4 FY11 Q1 FY12 Adjust Q1 FY12

Revenues $ 131.0 $—$ 131.0 $ 120.2 $—$ 120.2

Cost of revenues 84.0 (1.6) 82.4 79.9 (0.4) 79.5

Gross profit 47.0 1.6 48.6 40.3 0.4 40.7

Operating expense:

Research & development 11.5 —11.5 11.9 —11.9

Selling, general & administrative 28.1 (0.7) 27.4 26.7 (0.2) 26.5

Restructuring 0.5 (0.5)—0.2 (0.2) -

40.1 (1.2) 38.9 38.8 (0.4) 38.4

Operating profit (loss) 6.9 2.8 9.7 1.5 0.8 2.3

Interest income, net 0.3 —0.3 0.3 —0.3

Sale of contract manufacturing business——— —-

Other, net 0.4 —0.4 0.3 —0.3

Income before taxes, joint ventures and minority interest 7.6 2.8 10.4 2.1 0.8 2.9

Income tax provision (3.4) 2.8 (0.6) 0.3 —0.3

Net income before joint ventures and minority interest 11.0 —11.0 1.8 0.8 2.6

Joint venture income (losses) 1.1 —1.1 1.2 —1.2

Net income 12.1 —12.1 3.0 0.8 3.8

Net (income) loss attributable to minority interests (0.0) —(0.0) (0.0) —(0.0)

Net income (loss) attributable to Brooks $ 12.1 $—$ 12.1 $ 3.0 $ 0.8 $ 3.8

Basic earnings per share attributable to Brooks $ 0.19 $—$ 0.19 $ 0.05 $ 0.01 $ 0.06

Diluted earnings per share attributable to Brooks $ 0.19 $—$ 0.19 $ 0.05 $ 0.01 $ 0.06

Basic shares for EPS 64,750 64,750 64,750 64,812 64,812 64,812

Diluted shares for EPS 65,118 65,118 65,118 65,309 65,309 65,309

Adjustments

Cost of revenues

Purchasing accounting adjustments to sales contracts $ (1.0) $ (0.4)

Inventory charges recorded for acquisitions (0.6) —

$ (1.6) $ (0.4)

Operating expense:

Merger costs $ (0.7) $ (0.2)

Restructuring (0.5) (0.2)

$ (1.2) $ (0.4)

Income tax provision

One-time benefit from uncertain tax positions $ 2.8 $—