Brooks Automation, Inc. 4 th Quarter Fiscal 2013 Financial Results Conference Call

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Brooks Automation, Inc. 4 th Quarter Fiscal 2013 Financial Results Conference Call November 14, 2013

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 September 30, 2012. 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 fourth quarter financial results press release issued on November 14, 2013 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 website at www.brooks.com. 2

Gross Margin Expands 240 bps $ millions Q3 FY13 Q4 FY13 Change Revenue $118.1 $118.2 $ 0.1 Gross profit * 40.7 43.6 2.9 Gross margin % * 34.5% 36.9% 2.4% Research & development 12.1 13.3 (1.2) Selling, general & administrative * 21.1 24.5 (3.4) Non-GAAP Operating Profit * $ 7.5 $ 5.8 $(1.7) * Non GAAP measure. See appendix for a reconciliation to the appropriate GAAP measure. 3

Revenue and Operating Profit Waterfall $ millions Revenue Operating Profit Non-GAAP* 3 rd Quarter Fiscal 2013 $118.1 $ 7.5 Brooks Product Solutions (3.4) 1.3 Brooks Life Science Systems 2.5 (1.4) Brooks Global Services 1.0 (0.3) Other Operating Expenses - (1.3) 4 th Quarter Fiscal 2013 $118.2 $ 5.8 * Non GAAP measure. See appendix for a reconciliation to the appropriate GAAP measure. 4

GAAP and Adjusted Earnings $ millions Q3FY13 Q4FY13 Change Revenue $118.1 $118.2 $ 0.1 6 Operating profit (before amortization and special charges 7.5 5.8 (1.7) Amortization (2.4) (2.5) (0.1) Special Charges* (0.7) (2.7) (2.0) Other items 0.6 1.1 0.5 Income tax provision (benefit) 3.7 (2.1) 5.8 Minorities & joint venture earnings 0.2 2.2 2.0 Net income attributable to Brooks $ 1.5 $ 6.0 $ 4.5 GAAP Diluted Earnings per Share $0.02 $ 0.09 $ 0.07 Non GAAP Diluted Earnings per Share * $0.05 $ 0.13 $ 0.08 5 * Non GAAP measure. See appendix for a reconciliation to the appropriate GAAP measure.

Fiscal 2013 Q4 Cash and Cash Flows $ millions Adjusted EBITDA * $ 13.4 Working Capital movements 10.8 Dividend from Joint Venture 0.4 Other operating items 0.2 Cash Flow from Operations 24.8 Capital expenditures (0.9) Dividends (5.3) Other (Building Sale Proceeds $10.9; Acquisition ($9.3) ) 4.0 Net Change in Cash and Marketable Securities 22.6 Cash and Marketable Securities at September 30, 2013 $173.4 6 * Non GAAP measure. See appendix for a reconciliation to the appropriate GAAP measure.

September 2013 Condensed Balance Sheet CASH & MARKETABLE SECURITIES $173 $ Millions COMMENTS Accounts Receivable, net Inventories 77 59 Days of Sales Outstanding 98 3.2 turns Accounts Payable (35) Deferred revenue (20) Customer up front payments for BLSS Other current assets (liabilities), net (11) Net Working Capital 109 Net Fixed Assets 48 Goodwill & other intangible assets 182 Q4 Building sale $6.1 million; $0.9 million capex in the quarter $9 million Matrical; $2 million intangibles impairment Other assets (liabilities), net 120 Deferred Tax Asset / Joint Ventures Shareholders Equity $633 7

Brooks Product Solutions - Sequential Performance $ millions Q3FY13 Q4FY13 Comments on Sequential Trends Revenue $86.6 $83.2 3% decline in Semi Gross Profit * 28.5 31.3 Operating Expense * 23.0 24.5 Gross margin 37.6%; + 4.7 pts Favorable cost and mix Increased R&D funding; Stock comp reversal in prior quarter Segment Operating Income * $5.5 $ 6.8 Operating margin 8.2% * Non GAAP measure. See appendix for a reconciliation to the appropriate GAAP measure. 8

Brooks Life Science Systems - Sequential Performance $ millions Q3FY13 Q4FY13 Revenue $8.8 $11.3 Gross Profit * 4.2 4.2 Operating Expense * 6.3 7.7 Comments on Sequential Trends Growth in stores; Matrical $0.9 million 37.2% gross margin; $0.5 million inventory charge Matrical infrastructure; R&D investment for Skadi Segment Operating Loss * $(2.1) $(3.5) Loss in line with expectations * Non GAAP measure. See appendix for a reconciliation to the appropriate GAAP measure. 9

Brooks Global Services - Sequential Performance $ millions Q3FY13 Q4FY13 Comments on Sequential Trends Revenue $22.7 $23.7 4.4% organic growth Gross Profit * 8.1 8.1 Gross margin 34.2% Operating Expense * 4.0 4.3 Stock comp reversal in prior quarter. Segment Operating Income * $ 4.1 $ 3.8 Operating margin 16% * Non GAAP measure. See appendix for a reconciliation to the appropriate GAAP measure. 10

Quarterly Revenue Trends Excluding Contract Manufacturing Business 150 120 $ millions Mid Point of guidance 90 60 30 0 Semi FE Products Industrial Adjacent Service Life Sciences 11 2013 Brooks Automation, 11 Inc. Proprietary Information

Revenue, EBITDA & Earnings Guidance Q4FY13 Q1FY14 Comments on Sequential Trends Revenue ($ millions) $118.2 $119- $124 BPS Semiconductor expected to be up ~15%; Seasonality impacting revenue to Industrial markets Adjusted EBITDA* $ 13.4 $11 - $15 Lower Joint Venture income Non-GAAP Diluted Earnings Per Share* $ 0.13 $0.04 - $0.07 Q1 Tax rate anticipated at 35%; GAAP Diluted Earnings Per Share $ 0.09 $0.01 - $0.04 Building sale benefit of $0.01 in Q4 * Non GAAP measure. See appendix for reconciliation of historical measure to GAAP measure 12 12

Brooks Automation, Inc. 4 th Quarter Fiscal 2013 Financial Results Conference Call November 14, 2013 13

GAAP to Non-GAAP Reconciliation Consolidated P&L Three Months Ended Three Months Ended June 30, 2013 September 30, 2013 In millions, except per share data GAAP Results Adjustments Non-GAAP Results GAAP Results Adjustments Non-GAAP Results Revenues $ 118.1 $ - 118.1 $ 118.2 $ - 118.2 Cost of revenues 78.4 (1.0) 77.4 77.7 (3.1) 74.6 Gross profit 39.7 1.0 40.7 40.5 3.1 43.6 Operating expenses Research and development 12.1-12.1 13.3-13.3 Selling, general and administrative 22.6 (1.4) 21.2 26.2 (1.7) 24.5 Restructuring charges 0.6 (0.6) - 0.4 (0.4) - Total operating expenses 35.3 (2.0) 33.3 39.9 (2.1) 37.8 Operating income 4.4 3.0 7.4 0.6 5.2 5.8 Interest income, net 0.2-0.2 0.2-0.2 Other income, net 0.4-0.4 0.9 (1.0) (0.1) Income before income taxes and equity in earnings of joint ventures 5.0 3.0 8.0 1.7 4.2 5.9 Income tax provision (benefit) 3.7 0.9 4.6 (2.1) 1.4 (0.7) Income before equity in earnings of joint ventures 1.3 2.1 3.4 3.8 2.8 6.6 Equity in earnings of joint ventures 0.2-0.2 2.2-2.2 Net income 1.5 2.1 3.6 6.0 2.8 8.8 Net (income) attributable to noncontrolling interests - - - - - - Net income attributable to Brooks Automation, Inc. $ 1.5 $ 2.1 $ 3.6 $ 6.0 $ 2.8 $ 8.8 Net income per share attributable to Brooks Automation, Inc. common stockholders Basic $ 0.02 $ 0.05 $ 0.09 $ 0.13 Diluted $ 0.02 $ 0.05 $ 0.09 $ 0.13 Shares used in computing earnings per share Basic 66,041 66,041 66,153 66,153 Diluted 66,687 66,687 66,902 66,902 14 Adjustments: Cost of revenues: Amortization of completed technology intangible assets $ (1.0) $ (1.1) Impairment of completed technology intangible assets - (1.9) Purchase accounting impact on inventory and contracts acquired - (0.1) $ (1.0) $ (3.1) Operating expenses: Amortization of customer relationships intangible assets $ (1.4) $ (1.4) Impairment of customer relationships intangible assets - (0.1) Restructuring charges (0.6) (0.4) Merger costs - (0.2) $ (2.0) $ (2.1) Other income, net: Gain on sale of building $ - $ (1.0) Income tax provision: Tax impact of non-gaap adjustments $ 0.9 $ 1.4

GAAP to Non-GAAP Reconciliation Segments Q4 Brooks Product Solutions Brooks Global Services Brooks Life Science Systems In millions GAAP Q4FY'13 Adjustment Non-GAAP Q4FY'13 GAAP Q4FY'13 Adjustment Non-GAAP Q4FY'13 GAAP Q4FY'13 Adjustment Non-GAAP Q4FY'13 Revenues $ 83.2 $ - $ 83.2 $ 23.7 $ - $ 23.7 $ 11.3 $ - $ 11.3 Cost of revenues 52.3 (0.4) 51.9 15.8 (0.2) 15.6 9.6 (2.5) 7.1 Gross profit 30.9 0.4 31.3 7.9 0.2 8.1 1.7 2.5 4.2 Operating expenses 24.5-24.5 4.3-4.3 7.7-7.7 Operating income $ 6.4 $ 0.4 $ 6.8 $ 3.6 $ 0.2 $ 3.8 $ (6.0) $ 2.5 $ (3.5) Adjustments: Amortization of completed technology $ (0.4) $ (0.2) $ (0.5) Impairment of completed technology - - (1.9) Purchase accounting impact on inventory and contracts acquired - - (0.1) $ (0.4) $ (0.2) $ (2.5) 15 2012 Brooks Automation, Inc. Proprietary Information

GAAP to Non-GAAP Reconciliation Segments Q3 Brooks Product Solutions Brooks Global Services Brooks Life Science Systems In millions GAAP Q3FY'13 Adjustment Non-GAAP Q3FY'13 GAAP Q3FY'13 Adjustment Non-GAAP Q3FY'13 GAAP Q3FY'13 Adjustment Non-GAAP Q3FY'13 Revenues $ 86.6 $ - $ 86.6 $ 22.7 $ - $ 22.7 $ 8.8 $ - $ 8.8 Cost of revenues 58.5 (0.4) 58.1 14.8 (0.2) 14.6 5.1 (0.5) 4.6 Gross profit 28.1 0.4 28.5 7.9 8.1 3.7 0.5 4.2 Operating expenses 23.0-23.0 3.9-3.9 6.2-6.2 Operating income $ 5.1 $ 0.4 $ 5.5 $ 4.0 $ - $ 4.2 $ (2.5) $ 0.5 $ (2.0) Adjustments: Amortization of completed technology $ (0.4) $ (0.2) $ (0.5) 16 2012 Brooks Automation, Inc. Proprietary Information

GAAP to Non-GAAP Reconciliation Adjusted EBITDA Three Months Ended In millions September 30, 2013 Net income attributable to Brooks Automation, Inc. $ 6.0 Less: Interest income (0.2) Add: Income tax provision (benefit) (2.1) Add: Depreciation 3.4 Add: Amortization of completed technology 1.1 Add: Impairment of completed technology 1.9 Add: Amortization of customer relationships and acquired intangible assets 1.4 Add: Impairment of customer relationships and acquired intangible assets 0.1 Add: Stock-based compensation 2.1 Add: Restructuring charges 0.4 Add: Purchase accounting impact on inventory and contracts acquired 0.1 Add: Merger costs 0.2 Less: Gain on sale of building (1.0) Adjusted EBITDA $ 13.4 17 2012 Brooks Automation, Inc. Proprietary Information