Exhibit 99.1

UNAUDITED PRO FORMA CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

The following unaudited pro forma condensed consolidated financial statements of Brooks Automation, Inc. (the “Company”) have been prepared to reflect the closing on June 28, 2011 of the sale of assets related to the Company’s contract manufacturing business, as described in Item 1.01 of the Company’s Current Report on Form 8-K filed with the Securities and Exchange Commission (the “SEC”) on April 26, 2011 and in Item 2.01 of the Company’s Current Report on Form 8-K filed with the SEC on June 29, 2011 (the “Asset Sale”).

The unaudited pro forma condensed consolidated statements of operations for the six months ended March 31, 2011 and the fiscal year ended September 30, 2010 are based on the Company’s historical consolidated statements of operations, and give effect to the Asset Sale as if it had occurred on October 1, 2009. The anticipated non-recurring after tax gain on the Asset Sale is not reflected in the unaudited pro forma condensed consolidated statements of operations. The unaudited pro forma condensed consolidated balance sheet as of March 31, 2011 is based on the Company’s historical balance sheet as of March 31, 2011, and gives effect to the Asset Sale as if it had occurred on March 31, 2011. The anticipated non-recurring after tax gain on the asset sale is reflected in the unaudited pro forma condensed consolidated balance sheet.

The unaudited pro forma condensed consolidated financial statements presented below are based on the assumptions and adjustments described in the accompanying notes and do not reflect any adjustments for non-recurring items, overhead and administrative expense reductions, or changes in operating strategies arising as a result of the Asset Sale. These unaudited pro forma condensed consolidated financial statements reflect the estimated net proceeds of the Asset Sale as an increase to cash and cash equivalents. The Company expects that it will utilize these funds in strategic investments that leverage its existing technology capabilities, particularly into market sectors other than wafer front end semiconductor capital equipment. The actual effect of the Asset Sale on the business, financial condition and results of operations of the Company, due to this and other factors, including those set forth in the Company’s most recent Annual Report on Form 10-K filed with the SEC, could differ materially from the pro forma adjustments presented herein. However, the Company’s management believes that the assumptions used and the adjustments made in this presentation are reasonable under the circumstances and given the information available.

The unaudited pro forma condensed consolidated financial statements are presented for illustrative purposes only and are not historical facts or necessarily indicative of the operating results or the financial position that would have been achieved had the Asset Sale been consummated as of the dates indicated or of the results that may be obtained in the future. Readers are cautioned not to place undue reliance on such information and the Company makes no representations regarding the information set forth below or its ultimate performance compared to it. These unaudited pro forma condensed consolidated financial statements and the accompanying notes should be read together with (1) the Company’s audited consolidated financial statements and the accompanying notes as of and for the fiscal year ended September 30, 2010, and Management’s Discussion and Analysis of Financial Condition and Results of Operations included in the Company’s Annual Report on Form 10-K for the fiscal year ended September 30, 2010, which was filed with the SEC on November 23, 2010 and (2) the Company’s unaudited condensed consolidated financial statements and accompanying notes as of and for the six months ended March 31, 2011 and Management’s Discussion and Analysis of Financial Condition and Results of Operations included in the Company’s Quarterly Report on Form 10-Q for the fiscal quarter ended March 31, 2011, which was filed with the SEC on May 5, 2011.

Brooks Automation, Inc.
Pro Forma Condensed Consolidated Statements of Operations
(Unaudited)
For the six months ended March 31, 2011

		Historical				Disposed				Pro Forma				Pro Forma
In thousands, except per share data		Brooks				Business (a)				Adjustments				Brooks
Revenues
Product		$	336,635			$	(95,013	)		$	—			$	241,622
Services			34,383				—				—				34,383
Total revenues			371,018				(95,013	)			—				276,005
Cost of revenues
Product			228,066				(81,781	)			—				146,285
Services			23,959				—				—				23,959
Total cost of revenues			252,025				(81,781	)			—				170,244
Gross profit			118,993				(13,232	)			—				105,761
Operating expenses
Research and development			18,340				(938	)			—				17,402
Selling, general and administrative			49,723				(3,650	)			(252	)(c)			45,821
Restructuring charges			460				—				—				460
Total operating expenses			68,523				(4,588	)			(252	)			63,683
Operating income			50,470				(8,644	)			252				42,078
Interest income, net			507				(1	)			—				506
Other income, net			417				64				—				481
Income before income taxes and equity in earnings of joint ventures			51,394				(8,581	)			252				43,065
Income tax provision (benefit)			2,023				(199	)(b)			—				1,824
Income before equity in earnings of joint ventures			49,371				(8,382	)			252				41,241
Equity in earnings of joint ventures			718				—				—				718
Net income		$	50,089			$	(8,382	)		$	252			$	41,959
Add: Net income attributable to noncontrolling interests			(18	)			—				—				(18	)
Net income attributable to Brooks Automation, Inc.		$	50,071			$	(8,382	)		$	252			$	41,941
Basic net income per share attributable to Brooks Automation, Inc. common stockholders		$	0.78			$	(0.13	)		$	—			$	0.65
Diluted net income per share attributable to Brooks Automation, Inc. common stockholders		$	0.77			$	(0.13	)		$	—			$	0.65
Shares used in computing earnings per share
Basic			64,388				64,388				64,388				64,388
Diluted			64,801				64,801				64,801				64,801

See Notes to Pro Forma Condensed Consolidated Financial Statements.

Brooks Automation, Inc.
Pro Forma Condensed Consolidated Statements of Operations
(Unaudited)
For the fiscal year ended September 30, 2010

		Historical				Disposed				Pro Forma				Pro Forma
In thousands, except per share data		Brooks				Business (a)				Adjustments				Brooks
Revenues
Product		$	532,174			$	(155,542	)		$	—			$	376,632
Services			60,798				—				—				60,798
Total revenues			592,972				(155,542	)			—				437,430
Cost of revenues
Product			377,599				(138,053	)			—				239,546
Services			49,078				—				—				49,078
Total cost of revenues			426,677				(138,053	)			—				288,624
Gross profit			166,295				(17,489	)			—				148,806
Operating expenses
Research and development			31,162				(1,991	)			—				29,171
Selling, general and administrative			85,597				(7,163	)			—				78,434
Restructuring charges			2,529				—				—				2,529
Total operating expenses			119,288				(9,154	)			—				110,134
Operating income			47,007				(8,335	)			—				38,672
Interest income, net			1,041				(3	)			—				1,038
Other income, net			8,016				16				—				8,032
Income before income taxes and equity in earnings of joint ventures			56,064				(8,322	)			—				47,742
Income tax provision (benefit)			(2,746	)			(276	)(b)			—				(3,022	)
Income before equity in earnings of joint ventures			58,810				(8,046	)			—				50,764
Equity in earnings of joint ventures			215				—				—				215
Net income		$	59,025			$	(8,046	)		$	—			$	50,979
Add: Net income attributable to noncontrolling interests			(43	)			—				—				(43	)
Net income attributable to Brooks Automation, Inc.		$	58,982			$	(8,046	)		$	—			$	50,936
Basic net income per share attributable to Brooks Automation, Inc. common stockholders		$	0.92			$	(0.13	)		$	—			$	0.80
Diluted net income per share attributable to Brooks Automation, Inc. common stockholders		$	0.92			$	(0.13	)		$	—			$	0.79
Shares used in computing earnings per share
Basic			63,777				63,777				63,777				63,777
Diluted			64,174				64,174				64,174				64,174

See Notes to Pro Forma Condensed Consolidated Financial Statements.

Brooks Automation, Inc.
Pro Forma Condensed Consolidated Balance Sheet
(Unaudited)
As of March 31, 2011

		Historical				Disposed				Pro Forma
In thousands		Brooks				Business (d)				Brooks
Assets
Current assets
Cash and cash equivalents		$	59,328			$	75,430	(e)		$	134,758
Restricted cash			3,788				—				3,788
Marketable securities			59,540				—				59,540
Accounts receivable, net			99,646				(11,648	)			87,998
Inventories, net			126,615				(39,452	)			87,163
Prepaid expenses and other current assets			6,372				(260	)			6,112
Total current assets			355,289				24,070				379,359
Property, plant and equipment, net			60,499				(1,186	)			59,313
Long-term marketable securities			55,832				—				55,832
Goodwill			48,138				—				48,138
Intangible assets, net			9,265				—				9,265
Equity investment in joint ventures			33,535				—				33,535
Other assets			2,725				(141	)			2,584
Total assets		$	565,283			$	22,743			$	588,026
Liabilities and equity
Current liabilities
Accounts payable		$	61,042			$	(18,490	)		$	42,552
Deferred revenue			4,515				(607	)			3,908
Accrued warranty and retrofit costs			7,667				(494	)			7,173
Accrued compensation and benefits			12,919				(918	)			12,001
Accrued restructuring costs			1,553				—				1,553
Accrued income taxes payable			1,294				1,884	(f)			3,178
Accrued expenses and other current liabilities			10,051				(695	)			9,356
Total current liabilities			99,041				(19,320	)			79,721
Income taxes payable			12,974				—				12,974
Long-term pension liability			5,754				—				5,754
Other long-term liabilities			3,071				—				3,071
Total liabilities			120,840				(19,320	)			101,520
Equity
Common stock			796				—				796
Additional paid-in capital			1,805,799				—				1,805,799
Accumulated other comprehensive income			21,827				—				21,827
Treasury stock			(200,956	)			—				(200,956	)
Accumulated deficit			(1,183,578	)			42,063	(g)			(1,141,515	)
Total Brooks Automation, Inc. stockholders’ equity			443,888				42,063				485,951
Noncontrolling interest in subsidiaries			555				—				555
Total equity			444,443				42,063				486,506
Total liabilities and equity		$	565,283			$	22,743			$	588,026

See Notes to Pro Forma Condensed Consolidated Financial Statements.

Brooks Automation, Inc.
Notes to Pro Forma Condensed Consolidated Financial Statements
(Unaudited)