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): July 28, 2016

BROOKS AUTOMATION, INC.

(Exact Name of Registrant as Specified in Charter)

Delaware	0-25434	04-3040660
(State or Other Jurisdiction of Incorporation)	(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

N/A

(Former name or former address, if changed since last report.)

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 (see General Instruction A.2. below):

¨ 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 July 28, 2016, Brooks Automation, Inc. (“Brooks” or the “Company”) announced via press release its financial results for the fiscal quarter ended June 30, 2016. A copy of the press release is attached hereto as Exhibit 99.1.

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 July 28, 2016 by Brooks Automation, Inc.

SIGNATURE

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 W. Joseph
Date: July 28, 2016	Jason W. Joseph Vice President, General Counsel and Secretary

EXHIBIT INDEX

EXHIBIT NUMBER	DESCRIPTION OF EXHIBITS
99.1	Press release issued on July 28, 2016 by Brooks Automation, Inc.

EX-99.1

Exhibit 99.1

Brooks Automation Reports Fiscal Third Quarter 2016 Financial Results

CHELMSFORD, Mass., July 28, 2016 (GLOBE NEWSWIRE) -- Brooks Automation, Inc. (Nasdaq: BRKS), a leading worldwide provider of automation and cryogenic solutions for multiple markets including semiconductor manufacturing and life sciences, today reported financial results for the third fiscal quarter of 2016, ended June 30, 2016.

Fiscal Third Quarter of 2016 Financial and Operational Highlights:

• Revenue was $147.5 million;

• GAAP Net Income was $8.6 million with diluted EPS of $0.12;

• Non-GAAP Net Income was $11.1 million with diluted EPS of $0.16;

• Cash flow from operations was $15.7 million; and

• Total of Cash, Cash Equivalents, and Marketable Securities, as of June 30, 2016, was $72.2 million.

Summary of GAAP and Non-GAAP Earnings (Losses)

	Quarter Ended
	June 30,		March 31,			June 30,
Dollars in thousands, except per share data	2016		2016			2015
GAAP net income (loss)	$	8,564	$	(83,939	)	$	7,681
GAAP diluted earnings (loss) per share	$	0.12	$	(1.22	)	$	0.11
Non-GAAP net income	$	11,128	$	4,920		$	10,277
Non-GAAP diluted earnings per share	$	0.16	$	0.07		$	0.15

A reconciliation of non-GAAP measures to the most nearly comparable GAAP measures follows the consolidated balance sheets, statements of operations and statements of cash flows included in this release.

Management Comments

“Our strong third quarter performance highlights the strength of our portfolio and the improved earnings power of our revised organization structure. Sequential growth in automation, contamination control, BioStore systems, and BioStorage services has supported improved gross margins and cash flow,” commented Steve Schwartz, CEO of Brooks Automation. “Our Life Sciences business has continued to execute well, with growth coming from both large sample storage systems and BioStorage Technologies services. Both semiconductor and life sciences segments are on track to yield further growth and improve profits.”

GAAP Summary

Revenue increased 9% sequentially to $147.5 million in the third quarter of fiscal 2016, driven by a 10% increase in Life Sciences and a 9% increase in Brooks Semiconductor Solutions Group (formerly Brooks Product Solutions and Brooks Global Services). Gross margin was 36.7%, up 2.1 percentage points from the second fiscal quarter of 2016.  Operating expense of $45.7 million was 14% or $7.5 million less than the previous quarter primarily driven by lower restructuring charges.  In the third quarter, the Company incurred $1.0 million of restructuring charges compared to $7.3 million in the second quarter. The Company had a $0.2 million benefit from the reversal of accrued incentive based compensation for employees separated from the Company, compared to a $1.7 million similar benefit in the second quarter. GAAP net income was $8.6 million and diluted earnings per share was $0.12.

Beginning in the third quarter, the Company consolidated the operating results of Brooks Product Solutions (BPS) and Brooks Global Solutions (BGS) into one segment, referred to as Brooks Semiconductor Solutions Group, or BSSG, to better align with its new organizational structure and to reflect how strategic directions and resources are determined. The Brooks Life Sciences Systems (BLSS) segment remains unchanged.

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Amortization of intangibles, special charges, and one-time items are appropriately included in the GAAP summary of earnings.  The impact on earnings of these items is set out in the unaudited table included with this release.

Results of Q3 Fiscal 2016 (Non-GAAP Discussion)

Non-GAAP net income was $11.1 million in the third quarter, resulting in non-GAAP earnings per share of $0.16. This compares to non-GAAP net income of $4.9 million and non-GAAP earnings per share of $0.07 in the second quarter, and non-GAAP net income of $10.3 million and non-GAAP earnings per share of $0.15 in the third quarter of fiscal 2015.

As noted above, revenue for the third fiscal quarter of 2016 was $147.5 million, up 9% compared to the second fiscal quarter of 2016. The Brooks Semiconductor Solutions Group revenue increased 9% to $118.4 million, primarily driven by sales of Contamination Control Solutions of $15.8 million, up $9.6 million from the second quarter. Brooks Life Science Systems revenue grew 10% sequentially to $29.1 million, driven by 11% or $1.6 million sequential growth in the legacy business and 9% or $1.0 million growth in the recently acquired BioStorage services business, which reached $12.4 million of revenue in the quarter.

Adjusted gross margin, which excludes amortization, purchase accounting impacts and special charges, was 37.5% in the third quarter, up 2.2 percentage points from the prior quarter. The Semiconductor Solutions adjusted gross margin was 36.9% in the third quarter compared to 34.5% in the prior period, with improvements coming from both product and services lines. The Life Sciences adjusted gross margin was 40.0% in the third quarter compared to 38.5% in the prior period, with the legacy Life Sciences business delivering improved margins from large store systems. Gross margins for BioStorage Technologies were 43.9%, up 0.4 percentage points. In summary, the total adjusted gross profit increased by $7.6 million compared to the prior quarter, driven by revenue increases and gross margin improvements across both segments.

Bookings for the Semiconductor Solutions business in the third quarter totaled $115.2 million, compared to $108.6 million in the second quarter. The Life Sciences business booked a total of $40.6 million of new contract value in the quarter.

Non-GAAP operating expense of $41.8 million decreased $0.7 million sequentially, driven primarily by the restructuring actions initiated in the second quarter. The operating expense includes a benefit from the reversal of incentive based compensation accruals for employees departing in this quarter of $0.2 million, compared to $1.6 million in the second fiscal quarter.

Cash flow from operations was $15.7 million in the quarter and adjusted EBITDA was $19.0 million. The Company's cash, cash equivalents, and marketable securities increased $3.9 million to $72.2 million as of June 30, 2016, which reflects the operating cash flow, dividend payment and capital expenditures during the quarter.

Quarterly Cash Dividend

The Company additionally announced that the Board of Directors has approved a dividend of $0.10 per share payable on September 23, 2016 to stockholders of record on September 2, 2016. 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 Fourth Fiscal Quarter 2016

The Company announced revenue and earnings guidance for the fourth quarter of fiscal 2016. Revenue is expected to be in the range of $146 million to $151 million and non-GAAP diluted EPS is expected to be in the range of $0.14 to $0.17. (GAAP diluted EPS is projected to be $0.06 to $0.09, reflecting the impact of amortization, purchase price accounting, and anticipated restructuring charges.)

Conference Call

Brooks management will webcast its third quarter earnings conference call today at 5:30 p.m. Eastern Time. During the call, Company management will respond to questions concerning, but not limited to, the Company's financial performance, business conditions and industry outlook. Management's responses could contain information that has not been previously disclosed.

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The call will be broadcast live over the Internet and, together with presentation materials referenced on the call, will be 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 800-381-7839 (US & Canada only) or 212-231-2900 to listen to the live webcast.

About Brooks Automation, Inc.

Brooks is a leading worldwide provider of automation and cryogenic solutions for multiple markets including semiconductor manufacturing and life sciences. Brooks’ 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, Brooks has been a leading partner to the global semiconductor manufacturing market and, by applying expertise in automation and cryogenics, has expanded its offerings to meet the sample storage needs of customers in the life sciences industry. Brooks recently completed a strategic acquisition of BioStorage Technologies, Inc., complementing Brooks’ life sciences offerings with comprehensive outsource services.  Brooks now offers, in addition to a broad range of products and services for on-site infrastructure for sample management in temperatures of -20°C to -150°C, outsource service solutions across the complete life cycle of biological samples including collection, transportation, processing, storage, protection, retrieval and disposal.  Brooks is headquartered in Chelmsford, MA, with direct operations in North America, Europe and Asia. For more information, visitwww.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 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.

CONTACTS:

Lynne Yassemedis                    

Brooks Automation

978.262.2400

lynne.yassemedis@brooks.com

John Mills

Partner

ICR, LLC

646.277.1254

john.mills@icrinc.com

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BROOKS AUTOMATION, INC.

CONSOLIDATED BALANCE SHEETS

(unaudited)

(In thousands, except share and per share data)

	June 30, 2016			September 30, 2015
Assets
Current assets
Cash and cash equivalents	$	66,116		$	80,722
Marketable securities	18			70,021
Accounts receivable, net	101,091			86,448
Inventories	98,157			100,619
Deferred tax assets	3,958			17,609
Assets held for sale	2,806			2,900
Prepaid expenses and other current assets	21,078			15,158
Total current assets	293,224			373,477
Property, plant and equipment, net	54,763			41,855
Long-term marketable securities	6,068			63,287
Long-term deferred tax assets	1,125			70,476
Goodwill	202,386			121,408
Intangible assets, net	85,646			55,446
Equity method investments	26,530			24,308
Other assets	12,579			9,397
Total assets	$	682,321		$	759,654
Liabilities and Stockholders' equity
Current liabilities
Accounts payable	$	41,502		$	44,890
Deferred revenue	25,522			17,886
Accrued warranty and retrofit costs	5,955			6,089
Accrued compensation and benefits	18,031			20,401
Accrued restructuring costs	5,789			2,073
Accrued income taxes payable	7,168			6,111
Deferred tax liabilities	331			1,251
Accrued expenses and other current liabilities	17,751			15,550
Total current liabilities	122,049			114,251
Long-term tax reserves	2,714			3,644
Long-term deferred tax liabilities	6,962			3,196
Long-term pension liabilities	3,212			3,118
Other long-term liabilities	4,329			3,400
Total liabilities	139,266			127,609
Commitments and contingencies
Stockholders' equity
Preferred stock, $0.01 par value, 1,000,000 shares authorized, no shares issued or outstanding	—			—
Common stock, $0.01 par value, 125,000,000 shares authorized, 82,097,858 shares issued and 68,635,989 shares outstanding at June 30, 2016; 81,093,052 shares issued and 67,631,183 shares outstanding at September 30, 2015	821			811
Additional paid-in capital	1,851,292			1,846,357
Accumulated other comprehensive income	12,598			5,898
Treasury stock at cost- 13,461,869 shares	(200,956		)	(200,956		)
Accumulated deficit	(1,120,700		)	(1,020,065		)
Total stockholders' equity	543,055			632,045
Total liabilities and stockholders' equity	$	682,321		$	759,654

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BROOKS AUTOMATION, INC.

CONSOLIDATED STATEMENTS OF OPERATIONS

(unaudited)

(In thousands, except per share data)

	Three Months Ended June 30,						Nine Months Ended June 30,
	2016			2015			2016			2015
Revenue
Product	$	111,596		$	120,816		$	302,238		$	336,941
Services	35,938			24,078			100,532			70,002
Total revenue	147,534			144,894			402,770			406,943
Cost of revenue (a)
Product	69,557			77,128			192,816			221,877
Services	23,814			16,579			68,437			48,766
Total cost of revenue	93,371			93,707			261,253			270,643
Gross profit	54,163			51,187			141,517			136,300
Operating expenses
Research and development	12,819			12,834			39,208			39,001
Selling, general and administrative	31,854			27,825			98,667			86,845
Restructuring and other charges	996			358			9,807			3,711
Total operating expenses	45,669			41,017			147,682			129,557
Operating income (loss)	8,494			10,170			(6,165		)	6,743
Interest income	55			199			310			678
Interest expense	(37		)	(100		)	(56		)	(300		)
Other (loss) income, net	(107		)	460			(289		)	2,640
Income (loss) before income taxes and equity in earnings (losses) of equity method investments	8,405			10,729			(6,200		)	9,761
Income tax provision	220			3,340			75,070			1,790
Income (loss) income before equity in earnings (losses) of equity method investments	8,185			7,389			(81,270		)	7,971
Equity in earnings (losses) of equity method investments	379			292			1,248			(313		)
Net income (loss)	8,564			7,681			(80,022		)	7,658
Basic net income (loss) per share	$	0.12		$	0.11		$	(1.17	)	$	0.11
Diluted net income (loss) per share	$	0.12		$	0.11		$	(1.17	)	$	0.11
Dividend declared per share	$	0.10		$	0.10		$	0.30		$	0.30
Weighted average shares outstanding used in computing net (loss) income per share:
Basic	68,628			67,454			68,437			67,321
Diluted	69,166			68,571			68,437			68,520
(a) Periods ended June 30, 2016 on a year-to-date basis and June 30, 2015 on a quarter-to-date and year-to-date basis reflect a reclassification correction between the cost of service revenue and the cost of product revenue. Please refer to the Form 10-Q for the quarter ended June 30, 2016.

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BROOKS AUTOMATION, INC.

CONSOLIDATED STATEMENTS OF CASH FLOWS

(unaudited)

(In thousands)

	Nine months ended June 30,
	2016			2015
Cash flows from operating activities
Net (loss) income	$	(80,022	)	$	7,658
Adjustments to reconcile net (loss) income to net cash provided by operating activities:
Depreciation and amortization	21,320			18,929
Stock-based compensation	8,206			9,510
Amortization of premium on marketable securities and deferred financing costs	368			917
Undistributed (earnings) losses of equity method investments	(1,248		)	313
Deferred income tax provision (benefit)	71,875			(2,262		)
Gain on disposal of long-lived assets	—			(4		)
Changes in operating assets and liabilities, net of acquisitions:
Accounts receivable	2,862			(19,070		)
Inventories	2,110			(1,519		)
Prepaid expenses and other current assets	(3,909		)	(4,881		)
Accounts payable	(4,689		)	11,600
Deferred revenue	7,171			(2,339		)
Accrued warranty and retrofit costs	(87		)	(320		)
Accrued compensation and benefits	(6,558		)	(1,907		)
Accrued restructuring costs	3,720			(660		)
Accrued expenses and other current liabilities	(5,010		)	5,506
Net cash provided by operating activities	16,109			21,471
Cash flows from investing activities
Purchases of property, plant and equipment	(9,414		)	(5,945		)
Purchases of marketable securities	(12,901		)	(58,991		)
Sales and maturities of marketable securities	139,388			74,515
Disbursement for a loan receivable	(1,491		)	—
Acquisitions, net of cash acquired	(125,498		)	(17,257		)
Proceeds from sales of property, plant and equipment	—			6
Purchases of other investments	(500		)	(5,000		)
Net cash used in investing activities	(10,416		)	(12,672		)
Cash flows from financing activities
Proceeds from issuance of common stock	948			867
Principal repayments of capital lease obligations	—			(368		)
Payment of deferred financing costs	(508		)	—
Common stock dividends paid	(20,613		)	(20,229		)
Net cash used in financing activities	(20,173		)	(19,730		)
Effects of exchange rate changes on cash and cash equivalents	(126		)	(3,513		)
Net decrease in cash and cash equivalents	(14,606		)	(14,444		)
Cash and cash equivalents, beginning of period	80,722			94,114
Cash and cash equivalents, end of period	$	66,116		$	79,670

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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 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. Tables reconciling GAAP to the non-GAAP measures are presented below.

							Quarter Ended
	June 30, 2016						March 31, 2016						June 30, 2015
Dollars in thousands, except per share data	$			Per Diluted Share			$			Per Diluted Share			$			Per Diluted Share
GAAP net (loss) income	$	8,564		$	0.12		$	(83,939	)	$	(1.22	)	$	7,681		$	0.11
Adjustments:
Purchase accounting impact on inventory and contracts acquired	125			—			250			—			—			—
Amortization of intangible assets	3,837			0.06			3,809			0.06			3,216			0.05
Restructuring charges	996			0.01			7,336			0.11			358			0.01
Gain on sale of a building	(55		)	—			—			—			—			—
Liquidation costs due to dissolution of joint venture	—			—			—			—			69			—
Merger costs	84			—			215			—			44			—
Change in valuation allowance against deferred tax assets	—			—			79,340			1.15			—			—
Tax effect of adjustments	(2,423		)	(0.04		)	(2,091		)	(0.03		)	(1,091		)	(0.02		)
Non-GAAP adjusted net income	11,128			0.16			4,920			0.07			10,277			0.15
Stock-based compensation, pre-tax	1,637			—			1,855			—			2,402			—
Tax rate	20		%	—			16		%	—			30		%	—
Stock-based compensation, net of tax (a)	1,318			0.02			1,556			0.02			1,677			0.03
Non-GAAP adjusted net income - excluding stock-based compensation	$	12,446		$	0.18		$	6,476		$	0.09		$	11,954		$	0.17
Shares used in computing non-GAAP diluted net (loss) income per share	—			69,166			—			69,101			—			68,571
(a) The tax rate represents the effective tax rate on non-GAAP taxable ordinary income. We expanded our disclosure to correct and clarify the after tax impact of stock-based compensation on Non-GAAP adjusted net income and diluted EPS. For additional information on the impact of this correction on prior periods, please refer to the conference call presentation included in Investor Relations section of the Brooks website at www.brooks.com.

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	Nine Months Ended
	June 30, 2016						June 30, 2015
Dollars in thousands, except per share data	$			Per Diluted Share			$			Per Diluted Share
GAAP net loss	$	(80,022	)	$	(1.17	)	$	7,658		$	0.11
Adjustments:
Purchase accounting impact on inventory and contracts acquired	499			0.01			1,511			0.02
Amortization of intangible assets	11,153			0.16			9,646			0.14
Impairment of equity method investments	—			—			681			0.01
Restructuring charges	9,807			0.14			3,711			0.05
Gain on sale of a building	(55		)	—			—			—
Liquidation costs due to dissolution of joint venture	—			—			69			—
Merger costs	3,295			0.05			432			0.01
Change in valuation allowance against deferred tax assets	79,340			1.16			—			—
Tax effect of adjustments	(6,723		)	(0.10		)	(4,559		)	(0.07		)
Non-GAAP adjusted net income	17,294			0.25			19,149			0.28
Stock-based compensation, pre-tax	8,206			—			9,510			—
Tax rate	24		%	—			30		%	—
Stock-based compensation, net of tax (a)	6,237			$	0.09		6,657			$	0.10
Non-GAAP adjusted net income - excluding stock-based compensation	$	23,531		$	0.34		$	25,806		$	0.38
Shares used in computing non-GAAP diluted net loss per share	—			68,437			—			68,520
(a) The tax rate represents the effective tax rate on non-GAAP taxable ordinary income. We expanded our disclosure to correct and clarify the after tax impact of stock-based compensation on Non-GAAP adjusted net income and diluted EPS. For additional information on the impact of this correction on prior periods, please refer to the conference call presentation included in Investor Relations section of the Brooks website at www.brooks.com.

	Quarter Ended
	June 30, 2016				March 31, 2016				June 30, 2015
Dollars in thousands	$		%		$		%		$		%
GAAP gross profit/gross margin percentage	$	54,163	36.7	%	$	46,800	34.6	%	$	51,187	35.3	%
Adjustments:
Amortization of intangible assets	1,083		0.7	%	718		0.5	%	1,299		0.9	%
Purchase accounting impact on inventory and contracts acquired	125		0.1	%	250		0.2	%	—		—
Non-GAAP adjusted gross profit/gross margin percentage	$	55,371	37.5	%	$	47,768	35.3	%	$	52,486	36.2	%

	Nine Months Ended
	June 30, 2016				June 30, 2015
Dollars in thousands	$		%		$		%
GAAP gross profit/gross margin percentage	$	141,517	35.1	%	$	136,300	33.5	%
Adjustments:
Amortization of intangible assets	3,097		0.8	%	3,903		1.0	%
Purchase accounting impact on inventory and contracts acquired	499		0.1	%	1,511		0.4	%
Non-GAAP adjusted gross profit/gross margin percentage	$	145,113	36.0	%	$	141,714	34.8	%

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	Quarter Ended									Nine Months Ended
	June 30,			March 31,			June 30,			June 30,			June 30,
Dollars in thousands	2016			2016			2015			2016			2015
GAAP net (loss) income	$	8,564		$	(83,939	)	$	7,681		$	(80,022	)	$	7,658
Adjustments:
Less: Interest income	(55		)	(50		)	(199		)	(310		)	(678		)
Add: Interest expense	37			16			100			56			300
Add: Income tax provision (benefit)	220			78,220			3,340			75,070			1,790
Add: Depreciation	3,633			3,596			2,979			10,167			9,281
Add: Amortization of completed technology	1,083			718			1,299			3,097			3,903
Add: Amortization of customer relationships and acquired intangible assets	2,754			3,091			1,917			8,056			5,743
Earnings (losses) before interest, taxes, depreciation and amortization	$	16,236		$	1,652		$	17,117		$	16,114		$	27,997

	Quarter Ended							Nine Months Ended
	June 30,			March 31,		June 30,		June 30,			June 30
Dollars in thousands	2016			2016		2015		2016			2015
Earnings (losses) before interest, taxes, depreciation and amortization	$	16,236		$	1,652	$	17,117	$	16,112		$	27,997
Adjustments:
Add: Stock-based compensation	1,637			1,855		2,402		8,206			9,510
Add: Restructuring charges	996			7,336		358		9,807			3,711
Add: Purchase accounting impact on inventory and contracts acquired	125			250		—		499			1,511
Less: Gain on sale of a building	(55		)	—		—		(55		)	—
Add: Liquidation of a joint venture	—			—		69		—			69
Add: Merger costs	84			215		44		3,295			432
Add: Impairment of equity method investments	—			—		—		—			681
Adjusted earnings before interest, taxes, depreciation and amortization	$	19,023		$	11,308	$	19,990	$	37,864		$	43,911

	Quarter Ended									Nine Months Ended
	June 30,			March 31,			June 30,			June 30,			June 30,
Dollars in thousands	2016			2016			2015			2016			2015
GAAP selling, general and administrative expenses	$	31,854		$	32,692		$	27,825		$	98,667		$	86,845
Adjustments:
Less: Amortization of customer relationships and acquired intangible assets	(2,754		)	(3,091		)	(1,917		)	(8,056		)	(5,743		)
Less: Merger costs	(84		)	(215		)	(44		)	(3,295		)	(432		)
Non-GAAP adjusted selling, general and administrative expenses	$	29,016		$	29,386		$	25,864		$	87,316		$	80,670
Research and development expenses	$	12,819		$	13,111		$	12,834		$	39,208		$	39,001
Non-GAAP adjusted operating expenses	$	41,835		$	42,497		$	38,698		$	126,524		$	119,671

9

	Brooks Semiconductor Solutions Group						Brooks Life Science Systems
	Quarter Ended						Quarter Ended
Dollars in thousands	June 30, 2016		March 31, 2016		June 30, 2015		June 30, 2016		March 31, 2016		June 30, 2015
GAAP gross profit	$	42,904	$	36,943	$	46,515	$	11,259	$	9,857	$	4,672
Adjustments:
Amortization of intangible assets	711		390		901		372		328		398
Purchase accounting impact on inventory and contracts acquired	125		250		—		—		—		—
Non-GAAP adjusted gross profit	$	43,740	$	37,583	$	47,416	$	11,631	$	10,185	$	5,070

	Brooks Semiconductor Solutions Group				Brooks Life Science Systems
	Nine Month Ended				Nine Month Ended
Dollars in thousands	June 30, 2016		June 30, 2015		June 30, 2016		June 30, 2015
GAAP gross profit	$	114,506	$	122,938	$	27,011	$	13,362
Adjustments:
Amortization of intangible assets	2,005		2,706		1,093		1,197
Purchase accounting impact on inventory and contracts acquired	500		551		—		960
Non-GAAP adjusted gross profit	$	117,011	$	126,195	$	28,104	$	15,519

	Brooks Semiconductor Solutions Group						Brooks Life Science Systems
	Quarter Ended						Quarter Ended
Dollars in thousands	June 30, 2016		March 31, 2016		June 30, 2015		June 30, 2016		March 31, 2016		June 31, 2015
GAAP gross margin	36.2	%	33.9	%	36.3	%	38.7	%	37.2	%	27.8	%
Adjustments:
Amortization of intangible assets	0.6	%	0.4	%	0.7	%	1.3	%	1.2	%	2.4	%
Purchase accounting impact on inventory and contracts acquired	0.1	%	0.2	%	—		—		—		—
Non-GAAP adjusted gross margin	36.9	%	34.5	%	37	%	40.0	%	38.5	%	30.2	%

10

	Brooks Semiconductor Solutions Group				Brooks Life Science Systems
	Nine Month Ended				Nine Month Ended
Dollars in thousands	June 30, 2016		June 30, 2015		June 30, 2016		June 30, 2015
GAAP gross margin	35.1	%	34.5	%	35.3	%	26.2	%
Adjustments:
Amortization of intangible assets	0.6	%	0.8	%	1.4	%	2.3	%
Purchase accounting impact on inventory and contracts acquired	0.2	%	0.2	%	—		1.9	%
Non-GAAP adjusted gross margin	35.9	%	35.5	%	36.8	%	30.4	%

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