1. Basis of Presentation

The unaudited consolidated financial statements of Brooks Automation, Inc. and its subsidiaries (“Brooks” or the “Company”) included herein have been prepared in accordance with generally accepted accounting principles, or GAAP. In the opinion of management, all material adjustments which are of a normal and recurring nature necessary for a fair presentation of the results for the periods presented have been reflected.

Certain information and footnote disclosures normally included in the Company’s annual consolidated financial statements have been condensed or omitted and, accordingly, the accompanying financial information should be read in conjunction with the consolidated financial statements and notes thereto contained in the Company’s Annual Report on Form 10-K, filed with the United States Securities and Exchange Commission (the “SEC”) for the fiscal year ended September 30, 2011. Certain reclassifications have been made in the prior period consolidated financial statements to conform to the current presentation.

Revision of Prior Period Financial Statements

In the third quarter of fiscal 2012, the Company identified prior period errors related to the accounting for its equity method investment in ULVAC Cryogenics, Inc. (“UCI”). Specifically, the Company determined that certain subsidiaries of UCI were not fully included in the results of UCI reported to the Company. Therefore the Company’s portion of these subsidiaries of the joint venture were not reflected within equity in earnings of joint ventures in the Company’s consolidated statements of operations or within equity investment in joint ventures in the Company’s consolidated balance sheets for the quarterly and annual periods beginning in the fiscal year ended September 30, 2006 through the quarterly period ended March 31, 2012. In evaluating whether the Company’s previously issued consolidated financial statements were materially misstated, the Company considered the guidance in Accounting Standard Codification (ASC) Topic 250, “Accounting Changes and Error Corrections,” ASC Topic 250-10-S99-1, “Assessing Materiality,” and ASC Topic 250-10-S99-2, “Considering the Effects of Prior Year Misstatements when Quantifying Misstatements in Current Year Financial Statements.” The Company concluded these errors were not material individually or in the aggregate to any of the prior reporting periods, and therefore, amendments of previously filed reports were not required. However, if the entire correction was recorded in the third quarter of 2012, the cumulative amount would be material in the year ended September 30, 2012 and would have impacted comparisons to prior periods. As such, the revisions for these corrections to the applicable prior periods are reflected in the financial information herein and will be reflected in future filings containing such financial information. The revision had no net impact on the Company’s consolidated statements of cash flows for any prior period.

The following table summarizes the effects of the error on the prior period financial statements (in thousands, except per share data):

Revised Consolidated Balance Sheet Amounts


	As of September 30, 2011
	As Previously Reported			Adjustment			As Revised
Equity investments in joint ventures	$	34,612		$	338		$	34,950
Total assets		636,620			338			636,958
Accumulated other comprehensive income		19,480			(2,156	)		17,324
Accumulated deficit		(1,110,599	)		2,494			(1,108,105	)
Total Brooks Automation, Inc. stockholders’ equity		518,009			338			518,347
Total equity		518,598			338			518,936
Total liabilities and equity		636,620			338			636,958

Revised Consolidated Statement of Operations Amounts


	Three Months Ended December 31, 2011							Three Months Ended March 31, 2012						Six Months Ended March 31, 2012
	As Previously Reported		Adjustment			As Revised		As Previously Reported		Adjustment		As Revised		As Previously Reported		Adjustment		As Revised
Equity in earnings of joint ventures	$	1,225	$	(175	)	$	1,050	$	195	$	235	$	430	$	1,420	$	60	$	1,480
Net income		3,006		(175	)		2,831		9,491		235		9,726		12,497		60		12,557
Net income attributable to Brooks Automation, Inc.		2,998		(175	)		2,823		9,486		235		9,721		12,484		60		12,544
Net income per share attributable to Brooks Automation, Inc. common shareholders:
Basic	$	0.05	$	(0.00	)	$	0.04	$	0.15	$	0.00	$	0.15	$	0.19	$	0.00	$	0.19
Diluted	$	0.05	$	(0.00	)	$	0.04	$	0.14	$	0.00	$	0.15	$	0.19	$	0.00	$	0.19


	Three Months Ended December 31, 2010						Three Months Ended March 31, 2011						Three Months Ended June 30, 2011
	As Previously Reported		Adjustment		As Revised		As Previously Reported		Adjustment		As Revised		As Previously Reported		Adjustment		As Revised
Equity in earnings of joint ventures	$	310	$	469	$	779	$	408	$	238	$	646	$	900	$	732	$	1,632
Net income		23,486		469		23,955		26,603		238		26,841		66,189		732		66,921
Net income attributable to Brooks Automation, Inc.		23,486		469		23,955		26,585		238		26,823		66,183		732		66,915
Net income per share attributable to Brooks Automation, Inc. common shareholders:
Basic	$	0.37	$	0.01	$	0.37	$	0.41	$	0.00	$	0.42	$	1.02	$	0.01	$	1.03
Diluted	$	0.36	$	0.01	$	0.37	$	0.41	$	0.00	$	0.41	$	1.02	$	0.01	$	1.03


	Three Months Ended September 30, 2011						Six Months Ended March 31, 2011						Nine Months Ended June 30, 2011
	As Previously Reported		Adjustment		As Revised		As Previously Reported		Adjustment		As Revised		As Previously Reported		Adjustment		As Revised
Equity in earnings of joint ventures	$	1,164	$	594	$	1,758	$	718	$	707	$	1,425	$	1,618	$	1,439	$	3,057
Net income		12,126		594		12,720		50,089		707		50,796		116,278		1,439		117,717
Net income attributable to Brooks Automation, Inc.		12,098		594		12,692		50,071		707		50,778		116,254		1,439		117,693
Net income per share attributable to Brooks Automation, Inc. common shareholders:
Basic	$	0.19	$	0.01	$	0.20	$	0.78	$	0.01	$	0.79	$	1.80	$	0.02	$	1.83

Diluted	$	0.19	$	0.01	$	0.20	$	0.77	$	0.01	$	0.78	$	1.79	$	0.02	$	1.81


	Year Ended September 30, 2011						Year Ended September 30, 2010						Year Ended September 30, 2009
	As Previously Reported		Adjustment		As Revised		As Previously Reported		Adjustment		As Revised		As Previously Reported			Adjustment		As Revised
Equity in earnings of joint ventures	$	2,782	$	2,033	$	4,815	$	215	$	859	$	1,074	$	(213	)	$	246	$	33
Net income (loss)		128,404		2,033		130,437		59,025		859		59,884		(227,773	)		246		(227,527	)
Net income (loss) attributable to Brooks Automation, Inc.		128,352		2,033		130,385		58,982		859		59,841		(227,858	)		246		(227,612	)
Net income (loss) per share attributable to Brooks Automation, Inc. common shareholders:
Basic	$	1.99	$	0.03	$	2.02	$	0.92	$	0.01	$	0.94	$	(3.62	)	$	0.00	$	(3.62	)
Diluted	$	1.97	$	0.03	$	2.01	$	0.92	$	0.01	$	0.93	$	(3.62	)	$	0.00	$	(3.62	)

Recently Enacted Accounting Pronouncements

In December 2010, the Financial Accounting Standards Board (“FASB”) issued an amendment to the accounting requirements of goodwill, which requires a qualitative approach to considering impairment for a reporting unit with zero or negative carrying value. On October 1, 2011 the Company adopted this standard, which had no impact on its financial position or results of operations.

In December 2010, the FASB issued an amendment to the accounting requirements of business combinations, which establishes accounting and reporting standards for pro forma revenue and earnings of the combined entity for the current and comparable reporting periods. On October 1, 2011 the Company adopted this standard, which had no impact on its financial position or results of operations.

In May 2011, the FASB issued updated accounting guidance related to fair value measurements and disclosures that result in common fair value measurements and disclosures between GAAP and International Financial Reporting Standards. This guidance includes amendments which change the wording used to describe many of the requirements in U.S. GAAP for measuring fair value and for disclosing information about fair value measurements. On January 1, 2012 the Company adopted this standard, which had no impact on its financial position or results of operations.

In June 2011, the FASB issued an amendment to the accounting guidance for presentation of comprehensive income. Under the amended guidance, a company may present the total of comprehensive income, the components of net income, and the components of other comprehensive income either in a single continuous statement of comprehensive income or in two separate but consecutive statements. This authoritative guidance eliminates the option to present the components of other comprehensive income as part of the statement of changes in stockholder’s equity. This amendment is effective for annual periods beginning after December 15, 2011. Other than a change in presentation, the adoption of this guidance will not have an impact on the Company’s financial position or results of operations.

In September 2011, the FASB issued revised guidance intended to simplify how an entity tests goodwill for impairment. The amendment will allow an entity to first assess qualitative factors to determine whether it is necessary to perform the two-step quantitative goodwill impairment test. An entity no longer will be required to calculate the fair value of a reporting unit unless the entity determines, based on a qualitative assessment, that it is more likely than not that its fair value is less than its carrying amount. On October 1, 2011 the Company adopted this standard, which had no impact on its financial position or results of operations.