Azenta (AZTA) 10-Q 8 May 14 2014 Q2 Quarterly report Financial data

Document_and_Entity_Informatio

Document and Entity Information	6 Months Ended
	Mar. 31, 2014	Apr. 30, 2014
Document and Entity Information [Abstract]	'	'
Trading Symbol	'BRKS	'
Entity Registrant Name	'BROOKS AUTOMATION INC	'
Entity Central Index Key	'0000933974	'
Current Fiscal Year End Date	'--09-30	'
Entity Filer Category	'Large Accelerated Filer	'
Document Type	'10-Q	'
Document Period End Date	31-Mar-14	'
Document Fiscal Year Focus	'2014	'
Document Fiscal Period Focus	'Q2	'
Amendment Flag	'false	'
Entity Common Stock, Shares Outstanding	'	66,806,263

CONSOLIDATED_BALANCE_SHEETS

CONSOLIDATED BALANCE SHEETS (USD $)	Mar. 31, 2014	Sep. 30, 2013
In Thousands, unless otherwise specified
Current assets	'	'
Cash and cash equivalents	$85,281	$82,971
Restricted cash	0	177
Marketable securities	50,274	45,900
Accounts receivable, net	83,440	77,483
Inventories	93,750	94,411
Deferred tax assets	16,082	16,839
Assets held for sale	28,023	27,778
Prepaid expenses and other current assets	12,489	9,030
Total current assets	369,339	354,589
Property, plant and equipment, net	52,759	47,506
Long-term marketable securities	56,668	44,491
Long-term deferred tax assets	97,422	99,146
Goodwill	97,863	97,924
Intangible assets, net	55,124	60,088
Equity investment in joint ventures	30,342	25,687
Other assets	7,704	7,332
Total assets	767,221	736,763
Current liabilities	'	'
Accounts payable	35,672	35,392
Less current portion of capital lease obligation	881	0
Deferred revenue	33,116	19,610
Accrued warranty and retrofit costs	6,319	7,260
Accrued compensation and benefits	16,992	14,225
Accrued restructuring costs	1,552	1,412
Accrued income taxes payable	1,246	1,077
Liabilities held for sale	107	132
Accrued expenses and other current liabilities	16,979	13,453
Total current liabilities	112,864	92,561
Long-term capital lease obligation	7,656	0
Income taxes payable	7,673	7,036
Long-term pension liability	837	815
Other long-term liabilities	3,790	3,695
Total liabilities	132,820	104,107
Contingencies (Note 16)	'	'
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, 80,268,132 shares issued and 66,806,263 shares outstanding at March 31, 2014, 80,039,104 shares issued and 66,577,235 shares outstanding at September 30, 2013	803	800
Additional paid-in capital	1,831,802	1,825,499
Accumulated other comprehensive income	21,873	22,604
Treasury stock at cost, 13,461,869 shares	-200,956	-200,956
Accumulated deficit	-1,019,945	-1,015,991
Total Brooks Automation, Inc. stockholders' equity	633,577	631,956
Noncontrolling interest in subsidiaries	824	700
Total equity	634,401	632,656
Total liabilities and equity	$767,221	$736,763

CONSOLIDATED_BALANCE_SHEETS_Pa

CONSOLIDATED BALANCE SHEETS (Parenthetical) (USD $)	Mar. 31, 2014	Sep. 30, 2013
Statement of Financial Position [Abstract]	'	'
Preferred stock, par value (USD per share)	$0.01	$0.01
Preferred stock, shares authorized	1,000,000	1,000,000
Preferred stock, shares issued	0	0
Preferred stock, shares outstanding	0	0
Common stock, par value (USD per share)	$0.01	$0.01
Common stock, shares authorized	125,000,000	125,000,000
Common stock, shares issued	80,268,132	80,039,104
Common stock, shares outstanding	66,806,263	66,577,235
Treasury stock, shares	13,461,869	13,461,869

CONSOLIDATED_STATEMENTS_OF_OPE

CONSOLIDATED STATEMENTS OF OPERATIONS (USD $)	3 Months Ended		6 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Mar. 31, 2014	Mar. 31, 2013	Mar. 31, 2014	Mar. 31, 2013
Revenues	'	'	'	'
Product	$102,534	$88,652	$195,664	$159,680
Services	23,366	20,830	47,308	41,308
Total revenues	125,900	109,482	242,972	200,988
Cost of revenues	'	'	'	'
Product	64,786	60,685	125,522	111,645
Services	16,816	15,714	32,261	29,979
Total cost of revenues	81,602	76,399	157,783	141,624
Gross profit	44,298	33,083	85,189	59,364
Operating expenses	'	'	'	'
Research and development	12,493	11,333	25,044	22,237
Selling, general and administrative	28,637	24,169	54,772	49,324
Restructuring and other charges	772	751	1,519	5,441
Total operating expenses	41,902	36,253	81,335	77,002
Operating income (loss)	2,396	-3,170	3,854	-17,638
Interest income	258	265	504	540
Interest expense	0	0	0	-1
Other income (expense), net	56	77	315	-16
Income (loss) before income taxes and equity in earnings (losses) of equity method investments	2,710	-2,828	4,673	-17,115
Income tax benefit	1,117	327	1,910	-3,559
Income (loss) before equity in earnings (losses) of joint ventures	1,593	-3,155	2,763	-13,556
Equity in earnings (losses) of joint ventures	510	-10	1,259	-16
Income (loss) from continuing operations	2,103	-3,165	4,022	-13,572
Income from discontinued operations, net of tax	1,162	2,654	2,739	3,842
Net income (loss)	3,265	-511	6,761	-9,730
Net income attributable to noncontrolling interests	-76	-27	-124	-44
Net income (loss) attributable to Brooks Automation, Inc.	$3,189	($538)	$6,637	($9,774)
Basic net income (loss) per share attributable to Brooks Automation, Inc. common stockholders:	'	'	'	'
Net income (loss) from continuing operations (USD per share)	$0.03	($0.05)	$0.06	($0.21)
Net income from discontinued operations, net of tax (USD per share)	$0.02	$0.04	$0.04	$0.06
Basic net income (loss) per share attributable to Brooks Automation, Inc. (USD per share)	$0.05	($0.01)	$0.10	($0.15)
Diluted net income (loss) per share attributable to Brooks Automation, Inc. common stockholders:	'	'	'	'
Net income (loss) from continuing operations (USD per share)	$0.03	($0.05)	$0.06	($0.21)
Net income from discontinued operations, net of tax (USD per share)	$0.02	$0.04	$0.04	$0.06
Diluted net income (loss) per share attributable to Brooks Automation, Inc. common stockholders (USD per share)	$0.05	($0.01)	$0.10	($0.15)
Dividend declared per share (USD per share)	$0.08	$0.08	$0.16	$0.16
Shares used in computing earnings (loss) per share	'	'	'	'
Basic (shares)	66,646	65,889	66,499	65,726
Diluted (shares)	67,505	65,889	67,383	65,726

CONSOLIDATED_STATEMENTS_OF_COM

CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME (LOSS) (USD $)	3 Months Ended		6 Months Ended
In Thousands, unless otherwise specified	Mar. 31, 2014	Mar. 31, 2013	Mar. 31, 2014	Mar. 31, 2013
Statement of Stockholders' Equity [Abstract]	'	'	'	'
Net income (loss)	$3,265	($511)	$6,761	($9,730)
Change in cumulative translation adjustment	-547	-6,908	-841	-6,378
Change in unrealized gain (loss) on marketable securities	22	-23	21	-152
Change in unrealized gain (loss) on cash flow hedges	-37	0	68	0
Actuarial gain (loss)	10	23	21	313
Pension settlement	0	0	0	87
Comprehensive loss	2,713	-7,419	6,030	-15,860
Comprehensive income attributable to noncontrolling interests	-76	-27	-124	-44
Comprehensive loss attributable to Brooks Automation, Inc.	$2,637	($7,446)	$5,906	($15,904)

CONSOLIDATED_STATEMENTS_OF_CAS

CONSOLIDATED STATEMENTS OF CASH FLOWS (USD $)	6 Months Ended
In Thousands, unless otherwise specified	Mar. 31, 2014	Mar. 31, 2013
Cash flows from operating activities	'	'
Net income (loss)	$6,761	($9,730)
Adjustments to reconcile net income (loss) to net cash provided by operating activities:	'	'
Depreciation and amortization	11,170	12,443
Impairment of assets	398	0
Stock-based compensation	6,516	5,010
Amortization of premium on marketable securities	610	661
Undistributed (earnings) losses of equity method investments	-1,259	16
Deferred income tax benefit	2,269	-3,387
Pension settlement	0	87
Loss on disposal of long-lived assets	39	-150
Changes in operating assets and liabilities, net of acquisitions and disposals:	'	'
Accounts receivable	-6,057	9,489
Inventories	276	13,734
Prepaid expenses and other current assets	1,546	-4,305
Accounts payable	248	-3,260
Deferred revenue	13,408	3,711
Accrued warranty and retrofit costs	-951	-1,154
Accrued compensation and benefits	2,730	-2,702
Accrued restructuring costs	141	195
Accrued expenses and other current liabilities	-2,194	-3,914
Net cash provided by operating activities	35,651	16,744
Cash flows from investing activities	'	'
Purchases of property, plant and equipment	-2,696	-1,578
Purchases of marketable securities	-63,561	-39,269
Sale/maturity of marketable securities	46,551	98,178
Other investment	-4,000	0
Acquisition, net of cash acquired	0	-59,005
Proceeds from the sale of property, plant and equipment	0	2,368
Payment of deferred leasing cost	0	-2,076
Decrease in restricted cash	177	763
Net cash provided by (used in) investing activities	-23,529	-619
Cash flows from financing activities	'	'
Proceeds from issuance of common stock, net of issuance costs	967	969
Common stock dividend paid	-10,800	-10,672
Net cash used in financing activities	-9,833	-9,703
Effects of exchange rate changes on cash and cash equivalents	21	-940
Net increase (decrease) in cash and cash equivalents	2,310	5,482
Cash and cash equivalents, beginning of period	82,971	54,639
Cash and cash equivalents, end of period	85,281	60,121
Supplemental disclosure of non-cash investing and financing activities:	'	'
Acquisition of buildings and land through capital lease	$8,537	$0

Basis_of_Presentation

Basis of Presentation	6 Months Ended
	Mar. 31, 2014
Organization, Consolidation and Presentation of Financial Statements [Abstract]	'
Basis of Presentation	'
	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 accounting principles generally accepted in the United States, or GAAP. All intercompany accounts and transactions have been eliminated. In the opinion of management, all material adjustments, which are of a normal and recurring nature, necessary for a fair presentation of the financial position results of operations for the periods presented have been reflected. The results of operations for the interim periods are not necessarily indicative of the results of operations to be expected for the full fiscal year.
	In the second quarter of 2014, the Company determined that its Granville-Phillips Gas Analysis & Vacuum Measurement ("Granville-Phillips") business met the criteria to be reported as a discontinued operation. As a result, the Company’s historical financial statements have been revised to present the operating results of Granville-Phillips as a discontinued operation. The results of operations from the Granville-Phillips business are presented as “Income from discontinued operations, net of tax” in the Consolidated Statements of Operations. Assets and liabilities identifiable within the Granville-Phillips business are reported as "Assets held for sale" and "Liabilities held for sale," respectively, in the Consolidated Balance Sheets. The discussion in the notes to these consolidated statements, unless otherwise noted, relate solely to the Company's continuing operations (See Note 3).
	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 audited 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, 2013 (the "2013 Annual Report on Form 10-K").
	Use of Estimates
	The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the financial statements and the reported amounts of revenue and expenses during the reporting period. Significant estimates are associated with accounts receivable, inventories, intangible assets, goodwill, deferred income taxes, warranty obligations, revenue recognized using the percentage of completion method and stock-based compensation expense on performance-based awards. The Company bases its estimates on historical experience and various other assumptions, including in certain circumstances future projections, that management believes to be reasonable under the circumstances. Although the Company regularly assesses these estimates, actual results could differ from those estimates. Changes in estimates are recorded in the period in which they become known.
	Recently Enacted Accounting Pronouncements
	In July 2013, the Financial Accounting Standards Board ("FASB") issued an amendment to the accounting guidance for presentation of unrecognized tax benefits. The prior guidance related to unrecognized tax benefits did not explicitly address financial statement presentation of unrecognized tax benefits when a net operating loss carryforward, a similar tax loss or a tax credit carryforward exists. The amended guidance eliminates the existing diversity in practice in the presentation of unrecognized tax benefits in these instances. Under the amended guidance, an unrecognized tax benefit, or a portion of an unrecognized tax benefit, will be presented in the financial statements as a reduction of a deferred tax asset when an operating loss carryforward, a similar tax loss or a tax credit carryforward exists, with limited exceptions. This amended guidance is effective for fiscal years beginning on or after December 15, 2013. The Company does not expect that the adoption of this guidance will have a material impact on its financial position or results of operations.
	In April 2014, the FASB issued an amendment to the accounting guidance for reporting discontinued operations. The amended guidance raises the threshold for disposals to qualify as a discontinued operation by requiring a component of an entity that is held for sale, or has been disposed of by sale, to represent a strategic shift that has or will have a major effect on operations and financial results. Under the amended guidance, a strategic shift could include the disposal of a major line of business, a major geographical area, a major equity method investment or other major parts of an entity. In addition, the new guidance allows companies to have significant continuing involvement and continuing cash flows with the discontinued operation. The amended guidance is effective for fiscal years beginning on or after December 15, 2014. Early adoption is permitted for disposals, or classifications as held for sale, that have not been previously reported in financial statements. The Company has not applied this amended guidance to the Granville-Phillips discontinued operation.

StockBased_Compensation

Stock-Based Compensation	6 Months Ended
	Mar. 31, 2014
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]	'
Stock-Based Compensation	'
	Stock-Based Compensation
	The Company may issue stock options and restricted stock which vest upon the satisfaction of a performance condition and/or a service condition. In addition, the Company issues shares to participating employees pursuant to an employee stock purchase plan.
	The following table reflects stock-based compensation expense, excluding amounts related to discontinued operations, recorded during the three and six months ended March 31, 2014 and 2013 (in thousands):
		Three months ended						Six months ended
		March 31,						March 31,
		2014			2013			2014			2013
	Restricted stock	$	3,683		$	2,341		$	6,293		$	4,672
	Employee stock purchase plan	112			117			225			244
		$	3,795		$	2,458		$	6,518		$	4,916
	The fair value per share of restricted stock is equal to the quoted price of the Company’s common stock on the date of grant, net of estimated forfeitures. The expense related to these awards is being recorded ratably over the vesting period. In addition, for stock-based awards where vesting is dependent upon achieving certain operating performance goals, the Company estimates the likelihood of achieving the performance goals.
	During the six months ended March 31, 2014, the Company granted 1,409,557 shares of restricted stock to members of senior management of which 601,432 shares vest over the service period. The vesting of the remaining 808,125 shares will vary based on the achievement of certain financial performance goals which will be measured at the end of fiscal year 2014, and a continuing required service period. Total compensation expense on both of these awards is a maximum of $19.2 million, net of cancellations. Changes to the projected attainment against performance targets during fiscal 2014 may result in an adjustment to the amount of cumulative compensation recorded as of the date the estimate is revised. Of the 1,409,557 shares of restricted stock that the Company granted, 8,500 shares were granted to Granville-Phillips employees.
	During the six months ended March 31, 2013, the Company granted 1,224,000 shares of restricted stock to members of senior management of which 546,625 shares vest over a required service period. The vesting of the remaining 677,375 shares depended upon the achievement of certain financial performance goals which were measured at the end of fiscal year 2013, and a continuing required service period. Based on the Company’s results for fiscal 2013 relative to the financial performance goals established in the grant, 460,615 of the 677,375 shares were earned. These awards will vest over the remaining service period. Total compensation expense on the awards granted during the six months ended March 31, 2013 is a maximum of $7.3 million, net of cancellations. However, the final compensation expense related to these awards is dependent on the award holders completing the remaining service period. Of the 1,224,000 shares of restricted stock that the Company granted, 29,380 shares were granted to Granville-Phillips employees.
	Stock Option Activity
	The following table summarizes stock option activity for the six months ended March 31, 2014:
		Number of		Weighted-		Weighted			Aggregate
		Options		Average		Average			Intrinsic Value
				Remaining		Exercise Price			(In Thousands)
				Contractual Term
	Outstanding at September 30, 2013	15,540				$	15.86
	Outstanding at March 31, 2014	15,540		0.3 years		$	15.86		$	—
	Vested at March 31, 2014	15,540		0.3 years		$	15.86		$	—
	Options exercisable at March 31, 2014	15,540		0.3 years		$	15.86		$	—
	Based on the Company’s closing stock price of $10.93 as of March 31, 2014, there was no intrinsic value to the option holders.
	No stock options were granted during the three or six months ended March 31, 2014 or 2013. There were no stock option exercises in the three or six months ended March 31, 2014. The total intrinsic value of options exercised during the three and six months ended March 31, 2013 was $19,000. The total cash received from participants as a result of stock option exercises during the three and six months ended March 31, 2013 was $67,000.
	As of March 31, 2014, there was no future compensation cost related to stock options as all outstanding stock options have vested.
	Restricted Stock Activity
	The following table summarizes restricted stock activity for the six months ended March 31, 2014:
		Shares		Weighted
				Average
				Grant-Date
				Fair Value
	Outstanding at September 30, 2013	2,915,413		$	11.25
	Awards granted	1,409,557		9.46
	Awards vested	(522,023	)	9.37
	Awards canceled	(767,962	)	10.63
	Outstanding at March 31, 2014	3,034,985		$	10.9
	The fair value of restricted stock awards vested during the three months ended March 31, 2014 and 2013 was $1.8 million and $3.1 million, respectively. The fair value of restricted stock awards vested during the six months ended March 31, 2014 and 2013 was $4.9 million and $6.0 million, respectively.
	As of March 31, 2014, the unrecognized compensation cost related to restricted stock that is expected to vest is $15.7 million and will be recognized over an estimated weighted average service period of 1.8 years.
	Employee Stock Purchase Plan
	A total of 115,132 shares were purchased under the employee stock purchase plan during the three and six months ended March 31, 2014 for aggregate proceeds of $1.0 million. A total of 115,751 shares were purchased under the employee stock purchase plan during the three and six months ended March 31, 2013 for aggregate proceeds of $1.0 million.

Acquisition

Acquisition	6 Months Ended
	Mar. 31, 2014
Business Combinations [Abstract]	'
Acquisition	'
	Acquisitions
	Acquisition of Matrical
	On August 1, 2013, the Company acquired certain assets and assumed certain liabilities of Matrical, Inc.’s ("Matrical") life science businesses (collectively “the Acquired assets”) for cash consideration of approximately $9.3 million, net of cash acquired. The acquisition of the Acquired assets provides the Company with the opportunity to enhance its existing product offerings in biobanking and sample management.
	The Company recorded the assets and liabilities associated with the purchase of the Acquired assets at their fair values as of the acquisition date. The amounts recorded were as follows (in thousands):
	Accounts receivable	$	636
	Inventory	2,095
	Prepaid and other current assets	103
	Property, plant and equipment	534
	Completed technology	500
	Customer relationships	1,500
	Goodwill	7,076
	Debt	(902		)
	Accounts payable	(294		)
	Deferred revenue	(351		)
	Customer deposits	(1,249		)
	Other current liabilities	(322		)
	Total purchase price, net of cash acquired	$	9,326
	In performing the purchase price allocation, the Company considered, among other factors, analyses of historical financial performance, its intention for future use of the Acquired assets, and estimates of future cash flows from the Acquired assets. The purchase price was allocated based upon the fair value of the identified assets acquired and liabilities assumed as of the acquisition date from a market participant’s perspective.
	The Company used the relief-from-royalty method to value the completed technology and the excess earnings method to value the customer relationships. Cash flows were discounted at a rate of 18%. The weighted-average amortization periods are 4.6 years for completed technologies and 7.0 years for customer relationships. The intangible assets acquired will be amortized using the straight-line method because it approximates the pattern in which the economic benefits are expected to be realized.
	Goodwill represents the excess of the purchase price over the fair values of the net tangible and intangible assets acquired and is primarily the result of expected synergies from combining the Matrical products with the Company's other life science products. Goodwill arising from the acquisition of the Acquired assets is deductible for tax purposes.
	The operating results of the Acquired assets have been included in the results of operations for the Brooks Life Science Systems segment from the date of acquisition.
	The Company completed the final allocation of the purchase price related to the Acquired assets in the first quarter of fiscal year 2014. Prior to finalizing the purchase price allocation in the first quarter of fiscal 2014, the Company made an adjustment to reduce the fair value of deferred revenue acquired in the acquisition and goodwill by $61,000.
	Acquisition of Crossing
	On October 29, 2012, the Company acquired all the outstanding stock of Crossing Automation Inc. (“Crossing”), a U.S. based provider of automation solutions and services primarily to global semiconductor front-end markets. The Company paid, in cash, an aggregate merger consideration of $59.0 million net of cash acquired. The acquisition of Crossing provides the Company with the opportunity to enhance its existing capabilities with respect to manufacturing of atmospheric and vacuum automation solutions within the semiconductor front-end market.
	The Company recorded the assets and liabilities associated with Crossing at their fair values as of the acquisition date. The amounts recorded were as follows (in thousands):
	Accounts receivable	$	5,356
	Inventory	8,668
	Prepaid expenses	1,968
	Property, plant and equipment	2,270
	Completed technology	10,530
	Customer relationships	20,010
	Goodwill	26,453
	Other long term assets	885
	Accounts payable	(3,024		)
	Accrued liabilities	(5,172		)
	Deferred revenue	(319		)
	Other current liabilities	(388		)
	Other long-term liabilities	(8,232		)
	Total purchase price, net of cash acquired	$	59,005
	In performing the purchase price allocation, the Company considered, among other factors, its intention for future use of the acquired assets, analyses of historical financial performance, and estimates of future cash flows from Crossing’s products and services. The purchase price was allocated based upon the fair value of the identified assets acquired and liabilities assumed as of the acquisition date from a market participant’s perspective.
	The Company used the relief-from-royalty method to value the completed technology and the excess earnings method to value the customer relationships. Cash flows were discounted at a rate of 15%. The weighted-average amortization periods are 7.7 years for completed technologies and 8.0 years for customer relationships. The intangible assets acquired will be amortized using methods that approximate the pattern in which the economic benefits are expected to be realized, including variable declining balance and straight-line methods.
	Goodwill is primarily the result of expected synergies from combining the operations of Crossing with the Company. Goodwill arising from the acquisition of Crossing is not deductible for tax purposes.
	The operating results of Crossing have been included in the results of operations for the Brooks Product Solutions and Brooks Global Services segments from the date of acquisition.
	The Company completed the final allocation of the purchase price related to Crossing in the fourth quarter of fiscal year 2013.

Discontinued_Operations

Discontinued Operations	6 Months Ended
	Mar. 31, 2014
Discontinued Operations and Disposal Groups [Abstract]	'
Discontinued Operations	'
	Discontinued Operations
	The Granville-Phillips business unit develops, manufactures, sells and services vacuum measurement and gas analysis instrumentation to semiconductor and non-semiconductor customers. On March 18, 2014, the Company announced an agreement to sell this business to MKS Instruments, Inc. for $87.0 million in cash. The sale is subject to regulatory approval and customary closing conditions. The Company expects to complete the sale in the quarter ending June 30, 2014. The Company determined that its Granville-Phillips business met the criteria to be reported as a discontinued operation. As a result, the Company’s historical financial statements have been revised to present the operating results of the Granville-Phillips business as a discontinued operation. Summarized results of the discontinued operation are as follows (in thousands):
		Three Months Ended					Six Months Ended
		March 31,					March 31,
		2014		2013			2014		2013
	Revenue	$	7,453	$	7,137		$	14,968	$	13,656
	Income from discontinued operations	$	1,825	$	2,198		$	4,309	$	3,602
	Income tax provision (benefit)	663		(456		)	1,570		(240		)
	Income from discontinued operations, net of tax	$	1,162	$	2,654		$	2,739	$	3,842
	Assets and liabilities identifiable within the Granville-Phillips business are reported as "Assets held for sale" and "Liabilities held for sale," respectively, in the Consolidated Balance Sheets. The major classes of assets and liabilities of the discontinued operation as are follows (in thousands):
		March 31,		September 30,
		2014		2013
	Inventory	$	3,602	$	3,308
	Property, plant and equipment	315		364
	Goodwill	24,106		24,106
	Assets held for sale	$	28,023	$	27,778
	Deferred revenue	$	21	$	43
	Accrued warranty and retrofit costs	86		89
	Liabilities held for sale	$	107	$	132
	Assets and liabilities held for sale are classified as current in the Consolidated Balance Sheets because the Company expects to complete the sale of the Granville-Phillips business in the third quarter of fiscal 2014.

Goodwill_and_Intangible_Assets

Goodwill and Intangible Assets	6 Months Ended
	Mar. 31, 2014
Goodwill and Intangible Assets Disclosure [Abstract]	'
Goodwill and Intangible Assets	'
	Goodwill and Intangible Assets
	Goodwill represents the excess of net book value over the estimated fair value of net tangible and identifiable intangible assets of a reporting unit. The Company performs an annual impairment test of its goodwill on September 30 of each fiscal year unless interim indicators of impairment exist. The Company did not identify any indicators of goodwill impairment during the six month period ended March 31, 2014 that would warrant an interim test.
	The components of the Company’s goodwill, excluding amounts related to the discontinued operations, by business segment at March 31, 2014 are as follows (in thousands):
		Brooks			Brooks			Brooks			Other			Total
		Product			Global			Life Science
		Solutions			Services			Systems
	Gross goodwill at September 30, 2013	$	482,637		$	156,792		$	47,439		$	26,014		$	712,882
	Less: aggregate impairment charges recorded	(437,706		)	(151,238		)	—			(26,014		)	(614,958		)
	Goodwill, less accumulated impairments at September 30, 2013	44,931			5,554			47,439			—			97,924
	Adjustments during the six months ended March 31, 2014	—			—			(61		)	—			(61		)
	Goodwill, less accumulated impairments at March 31, 2014	$	44,931		$	5,554		$	47,378		$	—		$	97,863
	Components of the Company’s identifiable intangible assets, excluding amounts related to the discontinued operations, are as follows (in thousands):
		31-Mar-14									September 30, 2013
		Cost			Accumulated			Net Book			Cost			Accumulated			Net Book
					Amortization			Value						Amortization			Value
	Patents	$	7,808		$	7,248		$	560		$	7,808		$	7,196		$	612
	Completed technology	53,557			39,211			14,346			57,050			40,354			16,696
	Trademarks and trade names	3,496			3,496			—			3,564			3,554			10
	Customer relationships	67,134			26,916			40,218			66,687			23,917			42,770
		$	131,995		$	76,871		$	55,124		$	135,109		$	75,021		$	60,088
	The Company is required to test certain long-lived assets when indicators of impairment are present. The Company determined that impairment indicators were present for the long-lived assets related to its Celigo product line as of September 30, 2013. The long-lived assets in question were tested for recoverability in the fourth quarter of fiscal year 2013 by comparing the sum of the undiscounted cash flows directly attributable to the assets to their carrying values, which resulted in the conclusion that the carrying amounts of the assets were not recoverable. The fair values of the assets were then evaluated to determine the amount of the impairment, if any. The fair value of the assets was based primarily on market-based valuation techniques. As a result of this analysis, management determined that an impairment loss of $2.0 million had occurred as of September 30, 2013, and allocated the loss to the long-lived assets in the impaired asset group based on the carrying value of each asset, with no asset reduced below its respective fair value.
	The Company revised its estimate of the fair value of these assets at December 31, 2013 and determined that an additional impairment loss of $0.4 million, representing the remaining carrying value of the long-lived assets, was required. The impairment charge was recorded as a component of cost of revenue in the Consolidated Statements of Operations during the first quarter of fiscal 2014. The Company completed the sale of the Celigo product line in the second quarter of fiscal 2014. The sale of the Celigo product line did not have a material impact on the Company's financial position or result of operations.

Income_Taxes

Income Taxes	6 Months Ended
	Mar. 31, 2014
Income Tax Disclosure [Abstract]	'
Income Taxes	'
	Income Taxes
	The Company recorded an income tax provision of $1.1 million and $1.9 million for the three and six months ended March 31, 2014, respectively. This tax provision substantially consists of U.S. and foreign income taxes, as well as interest related to unrecognized tax benefits.
	The Company recorded an income tax provision (benefit) of $0.3 million and $(3.6) million for the three and six months ended March 31, 2013, respectively. The tax provision for both periods includes $0.9 million of tax benefits recognized during the quarter ended March 31, 2013 resulting from the reinstatement of the U.S. federal research and development tax credit. The tax benefit for the six months ended March 31, 2013 is primarily driven by tax benefits generated on U.S. losses partially offset by a tax provision on income in foreign jurisdictions.
	The tax provision for the three months ended March 31, 2013 was calculated based on a quarterly loss. This unusual relationship between tax expense and pre-tax income was driven by a change in the estimated annual effective tax rate during the quarter which reduced the estimate of year-to-date tax benefits on the losses incurred during the first six months of the year.
	The Company evaluates the realizability of its deferred tax assets by jurisdiction and assesses the need for a valuation allowance on a quarterly basis. As of March 31, 2014, the Company has continued to maintain a valuation allowance in the U.S. against certain tax credits and state net operating losses due to the uncertainty of their realization based on long-term Company forecasts and the expiration dates on these attributes. The Company has also continued to maintain a valuation allowance in certain jurisdictions that have not generated historical cumulative profitability.
	The Company is subject to U.S. federal income tax and various state, local and foreign income taxes in various jurisdictions. The amount of income taxes paid is subject to the Company's interpretation of applicable tax laws in the jurisdictions in which it files. In the normal course of business, the Company is subject to examination by taxing authorities throughout the world. The Company has income tax audits in progress in various jurisdictions in which it operates. In the Company's U.S. and foreign jurisdictions, the years that may be examined vary, with the earliest tax year being 2006. Based on the outcome of these examinations, or the expiration of statutes of limitations for specific jurisdictions, the related unrecognized tax benefits could change from those recorded in the Company's Consolidated Balance Sheets. It is reasonably possible that the unrecognized tax benefit will be reduced by an amount in the range between $1.7 million and $2.8 million during the next twelve months as the result of the expiration of statutes of limitations and the settlement of foreign income tax audits.

Earnings_per_Share

Earnings per Share	6 Months Ended
	Mar. 31, 2014
Earnings Per Share [Abstract]	'
Earnings per Share	'
	Earnings per Share
	Below is a reconciliation of weighted average common shares outstanding for purposes of calculating basic and diluted earnings per share (in thousands):
		Three months ended		Six months ended
		March 31,		March 31,
		2014	2013	2014	2013
	Weighted average common shares outstanding used in computing basic earnings per share	66,646	65,889	66,499	65,726
	Dilutive common stock options and restricted stock awards	859	—	884	—
	Weighted average common shares outstanding for purposes of computing diluted earnings per share	67,505	65,889	67,383	65,726
	Options to purchase approximately 16,000 and 34,000 shares of common stock and 0 and 3,179,000 shares of restricted stock were excluded from the computation of diluted earnings per share attributable to common stockholders for the three months ended March 31, 2014 and 2013, respectively, as their effect would be anti-dilutive. In addition, options to purchase approximately 16,000 and 65,000 shares of common stock and 0 and 3,008,000 shares of restricted stock were excluded from the computation of diluted earnings per share attributable to common stockholders for the six months ended March 31, 2014 and 2013, respectively, as their effect would be anti-dilutive. All outstanding stock options and unvested shares of restricted stock were excluded from the computation of diluted earnings per share for the three and six months ended March 31, 2013 as a result of the net loss for those periods.

Segment_Information

Segment Information	6 Months Ended
	Mar. 31, 2014
Segment Reporting [Abstract]	'
Segment Information	'
	Segment Information
	The Company reports financial results in three segments: Brooks Product Solutions, Brooks Global Services and Brooks Life Science Systems. A description of segments is included in the 2013 Annual Report on Form 10-K.
	The Company evaluates performance and allocates resources based on revenues, operating income (loss) and returns on invested assets. Operating income (loss) for each segment includes selling, general and administrative expenses directly attributable to the segment. Other unallocated corporate expenses, amortization of acquired intangible assets (excluding completed technology) and restructuring and other charges are excluded from the segments’ operating income (loss). The Company’s indirect overhead costs, which include various general and administrative expenses, are allocated among the segments based upon multiple cost drivers associated with the respective administrative function, including segment revenue, segment headcount, or an analysis of the segments that benefit from a specific administrative function. Segment assets exclude cash, cash equivalents, restricted cash, marketable securities, deferred tax assets, assets held for sale and investments in equity method investments.
	Financial information for the Company’s business segments, excluding amounts related to the discontinued operations, is as follows (in thousands):
		Brooks			Brooks			Brooks			Total
		Product			Global			Life Science
		Solutions			Services			Systems
	Three months ended March 31, 2014
	Revenue
	Product	$	89,897		$	4,213		$	8,424		$	102,534
	Services	—			19,178			4,188			23,366
		$	89,897		$	23,391		$	12,612		$	125,900
	Gross profit	$	31,960		$	7,676		$	4,662		$	44,298
	Segment operating income (loss)	$	6,127		$	2,248		$	(3,565	)	$	4,810
	Three months ended March 31, 2013
	Revenue
	Product	$	78,563		$	3,731		$	6,358		$	88,652
	Services	—			18,073			2,757			20,830
		$	78,563		$	21,804		$	9,115		$	109,482
	Gross profit	$	24,313		$	6,359		$	2,411		$	33,083
	Segment operating income (loss)	$	1,464		$	1,799		$	(3,875	)	$	(612	)
	Six months ended March 31, 2014
	Revenue
	Product	$	171,453		$	7,652		$	16,559		$	195,664
	Services	—			39,058			8,250			47,308
		$	171,453		$	46,710		$	24,809		$	242,972
	Gross profit	$	60,461		$	15,501		$	9,227		$	85,189
	Segment operating income (loss)	$	10,455		$	5,091		$	(7,040	)	$	8,506
	Six months ended March 31 2013
	Revenue
	Product	$	134,990		$	7,236		$	17,454		$	159,680
	Services	—			35,509			5,799			41,308
		$	134,990		$	42,745		$	23,253		$	200,988
	Gross profit	$	39,293		$	11,366		$	8,705		$	59,364
	Segment operating income (loss)	$	(6,447	)	$	2,287		$	(3,897	)	$	(8,057	)
	Assets
	31-Mar-14	$	231,324		$	61,856		$	107,933		$	401,113
	September 30, 2013	$	226,759		$	59,762		$	105,221		$	391,742
	A reconciliation of the Company’s reportable segment operating income (loss) to the corresponding consolidated amounts for the three and six month periods ended March 31, 2014 and 2013 is as follows (in thousands):
		Three months ended						Six months ended
		March 31,						March 31,
		2014			2013			2014			2013
	Segment operating income (loss)	$	4,810		$	(612	)	$	8,506		$	(8,057	)
	Amortization of acquired intangible assets	1,460			1,413			2,916			2,856
	Restructuring and other charges	772			751			1,519			5,441
	Other unallocated corporate expenses	182			394			217			1,284
	Total operating income (loss)	$	2,396		$	(3,170	)	$	3,854		$	(17,638	)
	A reconciliation of the Company’s reportable segment assets to the corresponding consolidated amounts as of March 31, 2014 and September 30, 2013 is as follows (in thousands):
		March 31,			September 30,
		2014			2013
	Segment assets	$	401,113		$	391,742
	Cash, cash equivalents, restricted cash and marketable securities	192,223			173,539
	Deferred tax assets	113,504			115,985
	Assets held for sale	28,023			27,778
	Equity method investments	30,342			25,687
	Other unallocated corporate net assets	2,016			2,032
	Total assets	$	767,221		$	736,763

Significant_Customers

Significant Customers	6 Months Ended
	Mar. 31, 2014
Risks and Uncertainties [Abstract]	'
Significant Customers	'
	Significant Customers
	The Company had one customer that accounted for more than 10% of its revenue, at 10% and 13%, in each of the three months ended March 31, 2014 and 2013, respectively. The Company had one customer that accounted for more than 10% of revenue, at 12% and 11%, in each of the six months ended March 31, 2014 and 2013, respectively. The Company did not have any customers that accounted for more than 10% of its accounts receivable balance at March 31, 2014 or September 30, 2013.

Restructuring_and_Other_Charge

Restructuring and Other Charges	6 Months Ended
	Mar. 31, 2014
Restructuring and Related Activities [Abstract]	'
Restructuring and Other Charges	'
	Restructuring and Other Charges
	Restructuring charges in the three and six months ended March 31, 2014 consisted primarily of severance and other workforce-related costs and result from the consolidation of certain administrative functions in the Brooks Life Science Systems segment, the on-going transition of manufacturing certain of the Company’s Polycold products to a third party contract manufacturer and other programs designed to improve the Company’s cost structure.
	Total severance charges related to the outsourcing of the Polycold manufacturing operation are expected to be $1.1 million, including severance and retention fees. This charge is being recorded ratably over the period from notification of the closing to the actual service end date, or September 2014. The Company has expensed $0.8 million of the total charge as of March 31, 2014, and will expense the balance ratably through fiscal year 2014.
	Restructuring charges in the three and six months ended March 31, 2013 consisted of severance costs for workforce reductions implemented to consolidate the operations of Crossing and the Company, to transition the Polycold product line to a third party contract manufacturer and other programs designed to improve the Company’s cost structure. Restructuring charges also included costs to consolidate two of the Company's facilities in California. In addition, the Company incurred other charges of $0.1 million related to a partial settlement of a defined benefit pension plan that covers substantially all of the Company’s Swiss employees.
	The activity for the three and six months ended March 31, 2014 and 2013 related to the Company's restructuring-related accruals, excluding amounts related to the discontinued operations, is summarized below (in thousands):
		Activity — Three Months Ended March 31, 2014
		Balance at		Expense		Utilization			Balance at
		December 31,							March 31,
		2013							2014
	Facilities and other	$	57	$	7	$	(64	)	$	—
	Workforce-related	1,405		765		(618		)	1,552
		$	1,462	$	772	$	(682	)	$	1,552
		Activity - Three Months Ended March 31, 2013
		Balance at		Expense		Utilization			Balance at
		December 31,							March 31,
		2012							2013
	Facilities and other	$	265	$	112	$	(144	)	$	233
	Workforce-related	4,438		639		(2,746		)	2,331
		$	4,703	$	751	$	(2,890	)	$	2,564
		Activity — Six Months Ended March 31, 2014
		Balance at		Expense		Utilization			Balance at
		September 30,							March 31,
		2013							2014
	Facilities and other	$	155	$	13	$	(168	)	$	—
	Workforce-related	1,257		1,506		(1,211		)	1,552
		$	1,412	$	1,519	$	(1,379	)	$	1,552
		Activity — Six Months Ended March 31, 2013
		Balance at		Expense		Utilization			Balance at
		September 30,							March 31,
		2012							2013
	Facilities and other	$	—	$	690	$	(457	)	$	233
	Workforce-related	2,021		4,664		(4,354		)	2,331
		$	2,021	$	5,354	$	(4,811	)	$	2,564
	The Company anticipates that the accrued restructuring costs at March 31, 2014 will be paid in the next twelve months.

Employee_Benefit_Plans

Employee Benefit Plans	6 Months Ended
	Mar. 31, 2014
Compensation and Retirement Disclosure [Abstract]	'
Employee Benefit Plans	'
	Employee Benefit Plans
	The Company has two active defined benefit pension plans (collectively, the “Plans”). The Plans cover substantially all of the Company’s employees in Switzerland and Taiwan. Retirement benefits are generally earned based on years of service and compensation during active employment; however, the level of benefits varies within the Plans. Eligibility is determined in accordance with local statutory requirements.
	In connection with actions taken under the Company’s restructuring programs in the first quarter of fiscal 2013, the number of employees accumulating benefits under the Switzerland Plan declined significantly. As a result, a partial settlement event occurred and resulted in accelerated amortization of approximately $0.1 million of prior pension losses. The settlement loss, recorded in the quarter ended December 31, 2012, is included in restructuring and other charges in the Consolidated Statements of Operations.
	The components of the Company’s net pension cost for the three and six months ended March 31, 2014 and 2013 is as follows (in thousands):
		Three months ended						Six months ended
		March 31,						March 31,
		2014			2013			2014			2013
	Service cost	$	102		$	144		$	202		$	322
	Interest cost	39			35			78			80
	Amortization of losses	—			1			1			3
	Expected return on assets	(55		)	(58		)	(108		)	(135		)
	Net periodic pension cost	86			122			173			270
	Settlement loss	—			—			—			87
	Total pension cost	$	86		$	122		$	173		$	357

Capital_Lease_Obligation

Capital Lease Obligation	6 Months Ended
	Mar. 31, 2014
Leases [Abstract]	'
Capital Lease Obligation	'
	Capital Lease Obligation
	In March 2014, the Company exercised an option to renew the lease of a building and the related land on the Chelmsford, Massachusetts campus. The Company has leased this building since 2002. By exercising this option, the Company has also contracted to purchase the building at the end of the lease period. The assets acquired under the lease were recorded at the net present value of the minimum lease payments which was then allocated to the building and the land based on their relative fair values. The cost of the building and the land under the capital lease are included in the Consolidated Balance Sheets as property, plant and equipment at $6.4 million and $2.1 million, respectively. Depreciation expense related to the building is computed using the straight-line method over the estimated useful life of the asset.
	The obligation related to the capital lease is recorded as short-term or long-term obligation in the Consolidated Balance Sheets depending on when payments are due. The future minimum lease payments required under the capital lease and the present value of the net minimum lease payments, as of March 31, 2014, are as follows (in thousands):
	Year ended September 30,
	2014	$	441
	2015	881
	2016	881
	2017	881
	2018	6,901
	Total minimum lease payments	9,985
	Less amounts representing interest	1,448
	Total capital lease obligation	8,537
	Less current portion of capital lease obligation	881
	Long-term capital lease obligation	$	7,656

Other_Balance_Sheet_Informatio

Other Balance Sheet Information	6 Months Ended
	Mar. 31, 2014
Organization, Consolidation and Presentation of Financial Statements [Abstract]	'
Other Balance Sheet Information	'
	Other Balance Sheet Information
	The following is a summary of accounts receivable at March 31, 2014 and September 30, 2013 (in thousands):
		March 31,				September 30,
		2014				2013
	Accounts receivable	$	84,770			$	78,460
	Less allowance for doubtful accounts	(1,184		)		(863		)
	Less allowance for sales returns	(146		)		(114		)
		$	83,440			$	77,483
	The following is a summary of inventories at March 31, 2014 and September 30, 2013, excluding amounts related to the discontinued operations (in thousands):
		March 31,				September 30,
		2014				2013
	Inventories
	Raw materials and purchased parts	$	59,844			$	57,678
	Work-in-process	17,083				19,991
	Finished goods	16,823				16,742
		$	93,750			$	94,411
	Reserves for excess and obsolete inventory were $24.1 million, excluding amounts related to the discontinued operations, at March 31, 2014 and September 30, 2013.
	The Company provides for the estimated cost of product warranties, primarily from historical information, at the time product revenue is recognized and retrofit accruals at the time retrofit programs are established. The Company’s warranty obligation is affected by product failure rates, utilization levels, material usage, service delivery costs incurred in correcting a product failure, and supplier warranties on parts delivered to the Company.
	Product warranty and retrofit activity on a gross basis for the three and six months ended March 31, 2014 and 2013, excluding amounts related to the discontinued operations, is as follows (in thousands):
	Activity - Three Months Ended March 31, 2014
	Balance at				Adjustments for				Accruals		Costs Incurred			Balance at
	December 31,				Acquisitions and Divestitures									March 31,
	2013													2014
	$	6,762			$	—			$	2,275	$	(2,718	)	$	6,319
	Activity - Three Months Ended March 31, 2013
	Balance at				Adjustments for				Accruals		Costs Incurred			Balance at
	December 31,				Acquisitions and Divestitures									March 31,
	2012													2013
	$	7,637			$	—			$	2,985	$	(2,987	)	$	7,635
	Activity - Six Months Ended March 31, 2014
	Balance at				Adjustments for				Accruals		Costs Incurred			Balance at
	September 30,				Acquisitions and Divestitures									March 31,
	2013													2014
	$	7,260			$	—			$	4,150	$	(5,091	)	$	6,319
	Activity - Six Months Ended March 31, 2013
	Balance at				Adjustments for				Accruals		Costs Incurred			Balance at
	September 30,				Acquisitions and Divestitures									March 31,
	2012													2013
	$	7,246			$	962			$	5,317	$	(5,890	)	$	7,635

Joint_Ventures

Joint Ventures	6 Months Ended
	Mar. 31, 2014
Equity Method Investments and Joint Ventures [Abstract]	'
Equity Method Investments	'
	Equity Method Investments
	The Company accounts for its equity method investments using the equity method. Under this method of accounting, the Company records in income its proportionate share of the earnings (losses) of the investee with a corresponding increase (decrease) in the carrying value of the investment.
	BioCision, LLC
	In March 2014, the Company acquired a 22% equity interest in BioCision, LLC (“BioCision”), a privately-held company based in Larkspur, California, for $4.0 million. BioCision develops, manufactures and markets cell cryopreservation products used to improve biomaterial sample handling and standardization.
	ULVAC Cryogenics, Inc.
	The Company participates in a 50% joint venture, ULVAC Cryogenics, Inc. (“UCI”), with ULVAC Corporation of Chigasaki, Japan. UCI manufactures and sells cryogenic vacuum pumps, principally to ULVAC Corporation. For the three months ended March 31, 2014 and 2013, the Company recorded income (expense) associated with UCI of $0.5 million and $(16,000), respectively. For the six months ended March 31, 2014 and 2013, the Company recorded income associated with UCI of $1.2 million and $62,000, respectively. At March 31, 2014, the carrying value of UCI in the Company’s Consolidated Balance Sheet was $23.4 million. For each of the three months ended March 31, 2014 and 2013, management fee payments received by the Company from UCI were $0.1 million. For the six months ended March 31, 2014 and 2013, management fee payments received by the Company from UCI were $0.3 million and $0.2 million, respectively. For the three months ended March 31, 2014 and 2013, the Company incurred charges from UCI for products or services of $37,000 and $0.1 million, respectively. For the six months ended March 31, 2014 and 2013, the Company incurred charges from UCI for products or services of $0.1 million and $0.4 million, respectively. At March 31, 2014 and September 30, 2013, the Company owed UCI $27,000 and $26,000, respectively, in connection with accounts payable for unpaid products and services.
	Yaskawa Brooks Automation, Inc.
	The Company participates in a 50% joint venture with Yaskawa Electric Corporation (“Yaskawa”) called Yaskawa Brooks Automation, Inc. (“YBA”) to exclusively market and sell Yaskawa’s semiconductor robotics products and Brooks’ automation hardware products to semiconductor customers in Japan. For the three months ended March 31, 2014 and 2013, the Company recorded income associated with YBA of $35,000 and $6,000, respectively. For the six months ended March 31, 2014 and 2013, the Company recorded income (expense) associated with YBA of $17,000 and $(78,000), respectively. At March 31, 2014, the carrying value of YBA in the Company’s Consolidated Balance Sheet was $2.9 million. For the three months ended March 31, 2014 and 2013, revenue earned by the Company from YBA was $2.1 million and $1.3 million, respectively. For the six months ended March 31, 2014 and 2013, revenue earned by the Company from YBA was $2.8 million and $2.9 million, respectively. For each of the three months ended March 31, 2014 and 2013, the Company incurred charges from YBA for products or services of $0.2 million. For each of the six months ended March 31, 2014 and 2013, the Company incurred charges from YBA for products or services of $0.3 million.
	The amount due from YBA included in accounts receivable at March 31, 2014 and September 30, 2013 was $2.1 million and $2.3 million, respectively. At March 31, 2014 and September 30, 2013 the Company owed YBA $0 and $47,000 in connection with accounts payable for unpaid products and services.

Derivative_Instruments

Derivative Instruments	6 Months Ended
	Mar. 31, 2014
Derivative Instruments and Hedging Activities Disclosure [Abstract]	'
Derivative Instruments	'
	Derivative Instruments
	All derivatives, whether designated in a hedging relationship or not, are recorded on the Consolidated Balance Sheets at fair value. The accounting for changes in fair value of a derivative instrument depends on whether it has been designated and qualifies as part of a hedging relationship and further, on the type of hedging relationship. For those derivative instruments that are designated and qualify as hedging instruments, the Company must designate the hedging instrument, based on the exposure being hedged, as a fair value hedge, cash flow hedge or a hedge of a net investment in a foreign operation.
	A cash flow hedge is a derivative instrument designated for the purpose of hedging the exposure to variability in future cash flows resulting from a particular risk. If the derivative is designated as a cash flow hedge, the effective portions of changes in the fair value of the derivative are recorded in accumulated other comprehensive income and are recognized in the results of operations when the hedged item affects earnings. Ineffective portions of changes in the fair value of cash flow hedges are recognized in the results of operations.
	In June 2013, the Company entered into foreign exchange contracts to reduce its exposure to changes in foreign exchange rates associated with an order for multiple automated sample management systems. The Company concluded that these foreign currency contracts meet the criteria to qualify as a cash flow hedge. Accordingly, the Company is reflecting changes in the fair value of the effective portion of these foreign currency contracts in accumulated other comprehensive income. Amounts recorded in accumulated other comprehensive income will be reclassified to revenue in the Consolidated Statements of Operations when the forecasted transaction occurs.
	The Company had the following notional amounts outstanding under foreign currency contracts that qualify for cash flow hedge accounting at March 31, 2014 (in thousands):
	Buy Currency		Notional Amount			Sell Currency	Maturity		Notional Amount			Fair Value of		Fair Value of
			of Buy Currency in U.S. Dollars						of Sell Currency			Assets		Liabilities
									in U.S. Dollars
	U.S. Dollar		$	2,037		Japanese Yen	Apr-14		$	1,946		$	91	$	—
	The Company expects to classify the accumulated gain on these contracts into revenue in the third quarter of fiscal 2014. The Company did not recognize any amounts related to ineffectiveness in the results of operations for the six months ended March 31, 2014.
	In addition, the Company has various transactions and balances denominated in currencies other than the U.S. dollar. Most of these transactions or balances are denominated in Euros, British Pounds and a variety of Asian currencies. These transactions and balances, including short-term advances between the Company and its subsidiaries, subject the Company's operations to exposure from exchange rate fluctuations. The impact of currency exchange rate movement can be positive or negative in any period. The Company mitigates the impact of potential currency translation gains and losses on short-term intercompany advances through timely settlement of each transaction, generally within 30 days.
	The Company also enters into foreign exchange contracts to reduce its exposure to currency translation. Under forward contract arrangements, the Company typically agrees to purchase a fixed amount of U.S. Dollars in exchange for a fixed amount of a foreign currency on specified dates with maturities of three months or less. These transactions do not qualify for hedge accounting. For derivative instruments not designated as hedging instruments, changes in fair value are recognized in the Consolidated Statements of Operations as gains and losses consistent with the classification of the underlying risk.
	Net gains and losses recorded as a component of Other Income (Expense), net in the Consolidated Statements of Operations related to these contracts for the three and six month periods ended March 31, 2014 and 2013 is as follows (in thousands):
		Three Months Ended						Six Months Ended
		March 31,						March 31,
		2014			2013			2014			2013
	Realized gains (losses) on derivative instruments not designated as hedging instruments	$	(0.2	)	$	0.1		$	(0.1	)	$	0.1
	The Company had the following notional amounts outstanding under foreign currency contracts that do not qualify for hedge accounting at March 31, 2014 and September 30, 2013 (in thousands):
	March 31, 2014:
	Buy Currency		Notional Amount			Sell Currency	Maturity		Notional Amount			Fair Value of		Fair Value of
			of Buy Currency						of Sell Currency			Assets		Liabilities
									in U.S. Dollars
	U.S. Dollar		$	2,976		Japanese Yen	April to June 2014		$	2,973		$	3	$	—
	British Pound		2,470			Euro	April 2014		2,488			—		(18		)
	U.S. Dollar		698			Taiwan Dollar	April 2014		697			1		—
	Korean Won		605			U.S. Dollar	April 2014		602			3		—
	U.S. Dollar		428			Israeli Shekel	April 2014		431			—		(3		)
			$	7,177					$	7,191		$	7	$	(21	)
	September 30, 2013:
	Buy Currency		Notional Amount			Sell Currency	Maturity		Notional Amount			Fair Value of		Fair Value of
			of Buy Currency in U.S. Dollars						of Sell Currency			Assets		Liabilities
									in U.S. Dollars
	U.S. Dollar		$	2,770		Japanese Yen	October 2013 to December 2013		$	2,762		$	8	$	—
	Korean Won		686			U.S. Dollar	October 2013		688			—		2
	U.S. Dollar		301			Israeli Shekel	October 2013		304			—		3
	U.S. Dollar		231			Singapore Dollar	October 2013		231			—		—
			$	3,988					$	3,985		$	8	$	5
	The fair values of the forward contracts described above are recorded in the Company's Consolidated Balance Sheets as Prepaid Expenses and Other Current Assets and Accrued Expenses and Other Current Liabilities.

Marketable_Securities

Marketable Securities	6 Months Ended
	Mar. 31, 2014
Investments, Debt and Equity Securities [Abstract]	'
Marketable Securities	'
	Marketable Securities
	The Company invests its cash in marketable securities and classifies them as available-for-sale. The Company records these securities at fair value. Marketable securities reported as current assets represent investments that mature within one year from the balance sheet date. Long-term marketable securities represent investments with maturity dates greater than one year from the balance sheet date. At the time that the maturity dates of these investments become one year or less, the securities are reclassified to current assets. Unrealized gains and losses are excluded from earnings and reported in a separate component of stockholders’ equity until they are sold or mature. At the time of sale, any gains or losses, calculated by the specific identification method, will be recognized as a component of operating results.
	The following is a summary of marketable securities (included in short and long-term marketable securities in the Consolidated Balance Sheets), including accrued interest receivable, as of March 31, 2014 and September 30, 2013 (in thousands):
		Amortized		Gross		Gross			Fair Value
		Cost		Unrealized		Unrealized
				Gains		Losses
	March 31, 2014:
	U.S. Treasury securities and obligations of U.S. government agencies	$	15,876	$	3	$	(35	)	$	15,844
	Corporate securities	53,419		36		(30		)	53,425
	Mortgage-backed securities	1,035		31		—			1,066
	Other debt securities	899		—		—			899
	Municipal securities	23,882		11		(9		)	23,884
	Bank certificate of deposits	11,823		1		—			11,824
		$	106,934	$	82	$	(74	)	$	106,942
	September 30, 2013:
	U.S. Treasury securities and obligations of U.S. government agencies	$	19,528	$	6	$	(13	)	$	19,521
	Corporate securities	35,045		11		(47		)	35,009
	Mortgage-backed securities	1,093		25		(1		)	1,117
	Other debt securities	88		—		—			88
	Municipal securities	25,199		15		(7		)	25,207
	Bank certificate of deposits	9,451		—		(2		)	9,449
		$	90,404	$	57	$	(70	)	$	90,391
	The fair value of the marketable securities at March 31, 2014 by contractual maturity, are shown below (in thousands). Expected maturities could differ from contractual maturities because the issuers of the securities may have the right to prepay obligations without prepayment penalties.
		Fair Value
	Due in one year or less	$	50,274
	Due after one year through five years	53,291
	Due after ten years	3,377
		$	106,942

Fair_Value_Measurements

Fair Value Measurements	6 Months Ended
	Mar. 31, 2014
Fair Value Disclosures [Abstract]	'
Fair Value Measurements	'
	Fair Value Measurements
	The fair value measurement guidance establishes a fair value hierarchy which requires an entity to maximize the use of observable inputs and minimize the use of unobservable inputs when measuring fair value. The standard describes three levels of inputs that may be used to measure fair value:
	Level 1: Quoted prices in active markets for identical assets or liabilities as of the reporting date. Active markets are those in which transactions for the asset and liability occur in sufficient frequency and volume to provide pricing information on an ongoing basis.
	Level 2: Observable inputs other than Level 1 prices, such as quoted prices for similar assets or liabilities; quoted prices in markets that are not active; or other inputs that are observable or can be corroborated by observable market data for substantially the full term of the assets or liabilities.
	Level 3: Unobservable inputs that are supported by little or no market activity and that are significant to the fair value of the assets or liabilities.
	Assets and liabilities of the Company measured at fair value on a recurring basis as of March 31, 2014 and September 30, 2013 are summarized as follows (in thousands):
				Fair Value Measurements at Reporting Date Using
	Description	March 31,		Quoted Prices in		Significant Other		Significant
		2014		Active Markets for		Observable Inputs		Unobservable Inputs
				Identical Assets		(Level 2)		(Level 3)
				(Level 1)
	Assets
	Cash equivalents	$	6,532	$	16	$	6,516	$	—
	Available-for-sale securities	106,942		—		106,942		—
	Foreign exchange contracts	98		—		98		—
	Total Assets	$	113,572	$	16	$	113,556	$	—
	Liabilities
	Foreign exchange contracts	$	21	$	—	$	21	$	—
				Fair Value Measurements at Reporting Date Using
	Description	September 30,		Quoted Prices in		Significant Other		Significant
		2013		Active Markets for		Observable Inputs		Unobservable Inputs
				Identical Assets		(Level 2)		(Level 3)
				(Level 1)
	Assets
	Cash equivalents	$	7,754	$	6,152	$	1,602	$	—
	Available-for-sale securities	90,391		2,199		88,192		—
	Foreign exchange contracts	31		—		31		—
	Total Assets	$	98,176	$	8,351	$	89,825	$	—
	Liabilities
	Foreign exchange contracts	$	5	$	—	$	5	$	—
	Cash Equivalents
	Cash equivalents of $16,000 and $6.2 million at March 31, 2014 and September 30, 2013, respectively, consisting of Money Market Funds, are classified within Level 1 of the fair value hierarchy because they are valued using quoted market prices in active markets. Cash equivalents of $6.5 million and $1.6 million at March 31, 2014 and September 30, 2013, respectively, consisting of Bank Certificate of Deposits, U.S. Government Agency Securities and Municipal Securities, are classified within Level 2 of the hierarchy because they are not actively traded.
	Available-For-Sale Securities
	Available-for-sale securities of $2.2 million at September 30, 2013, consisting primarily of highly rated Corporate Bonds, are classified within Level 1 of the fair value hierarchy because they are valued using quoted market prices in active markets of identical assets or liabilities. Available-for-sale securities of $106.9 million and $88.2 million at March 31, 2014 and September 30, 2013, respectively, consisting of Municipal Securities, Bank Certificate of Deposits, Commercial Paper, U.S. Treasury Securities and Obligations of U.S. Government Agency Securities, and Mortgage-Backed Securities are classified within Level 2 of the fair value hierarchy because they are not actively traded and are valued using matrix pricing and benchmarking. Matrix pricing is a mathematical technique used to value securities by relying on the securities’ relationship to other benchmark quoted prices.
	Foreign Exchange Contracts
	Foreign exchange contract assets and liabilities are classified within Level 2 of the fair value hierarchy because there may not be an active market for each contract. However, the inputs used to calculate the value of the contract were obtained from an active market.

Contingencies

Contingencies	6 Months Ended
	Mar. 31, 2014
Commitments and Contingencies Disclosure [Abstract]	'
Commitments and Contingencies	'
	Commitments and Contingencies
	Letters of Credit
	At March 31, 2014, the Company had approximately $20.5 million of letters of credit outstanding that it issued.
	Contingencies
	The Company is subject to various legal proceedings, both asserted and unasserted, that arise in the ordinary course of business. The Company cannot predict the ultimate outcome of such legal proceedings or in certain instances provide reasonable ranges of potential losses. However, as of the date of this report, the Company believes that none of these claims will have a material adverse effect on its consolidated financial condition or results of operations. In the event of unexpected subsequent developments and given the inherent unpredictability of these legal proceedings, there can be no assurance that the Company's assessment of any claim will reflect the ultimate outcome and an adverse outcome in certain matters could, from time to time, have a material adverse effect on the Company's consolidated financial condition or results of operations in particular quarterly or annual periods.

Subsequent_Events

Subsequent Events	6 Months Ended
	Mar. 31, 2014
Subsequent Events [Abstract]	'
Subsequent Events	'
	Subsequent Event
	On April 30, 2014, the Company acquired all of the outstanding stock of DMS Dynamic Micro Systems Semiconductor Equipment GmbH (“DMS”), a German based provider of logistic solutions for semiconductor fabrication plants. The Company agreed to a purchase price of $31.0 million, subject to a working capital adjustment expected to be concluded within 90 days of closing. The aggregate merger consideration includes approximately $16.0 million related to the repayment of DMS’s debt obligations. The acquisition of DMS provides the Company with the opportunity to enhance its existing capabilities with respect to automation solutions in the semiconductor front-end market.
	On May 7, 2014, the Company’s Board of Directors declared a cash dividend of $0.08 per share payable on June 27, 2014 to common stockholders of record on June 6, 2014. Dividends are declared at the discretion of the Company’s Board of Directors and depend on actual cash from operations, the Company’s financial condition and capital requirements and any other factors the Company’s Board of Directors may consider relevant. Future dividend declarations, as well as the record and payment dates for such dividends, will be determined by the Company’s Board of Directors on a quarterly basis.

StockBased_Compensation_Tables

Stock-Based Compensation (Tables)	6 Months Ended
	Mar. 31, 2014
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]	'
Stock-Based Compensation Expense	'
	The following table reflects stock-based compensation expense, excluding amounts related to discontinued operations, recorded during the three and six months ended March 31, 2014 and 2013 (in thousands):
		Three months ended						Six months ended
		March 31,						March 31,
		2014			2013			2014			2013
	Restricted stock	$	3,683		$	2,341		$	6,293		$	4,672
	Employee stock purchase plan	112			117			225			244
		$	3,795		$	2,458		$	6,518		$	4,916
Stock Option Activity	'
	The following table summarizes stock option activity for the six months ended March 31, 2014:
		Number of		Weighted-		Weighted			Aggregate
		Options		Average		Average			Intrinsic Value
				Remaining		Exercise Price			(In Thousands)
				Contractual Term
	Outstanding at September 30, 2013	15,540				$	15.86
	Outstanding at March 31, 2014	15,540		0.3 years		$	15.86		$	—
	Vested at March 31, 2014	15,540		0.3 years		$	15.86		$	—
	Options exercisable at March 31, 2014	15,540		0.3 years		$	15.86		$	—
Status of Restricted Stock Activity and Changes	'
	The following table summarizes restricted stock activity for the six months ended March 31, 2014:
		Shares		Weighted
				Average
				Grant-Date
				Fair Value
	Outstanding at September 30, 2013	2,915,413		$	11.25
	Awards granted	1,409,557		9.46
	Awards vested	(522,023	)	9.37
	Awards canceled	(767,962	)	10.63
	Outstanding at March 31, 2014	3,034,985		$	10.9

Acquisition_Tables

Acquisition (Tables)	6 Months Ended
	Mar. 31, 2014
Business Combinations [Abstract]	'
Amounts of Assets and Liabilities at Fair Value as of Acquisition Date	'
	The Company recorded the assets and liabilities associated with Crossing at their fair values as of the acquisition date. The amounts recorded were as follows (in thousands):
	Accounts receivable	$	5,356
	Inventory	8,668
	Prepaid expenses	1,968
	Property, plant and equipment	2,270
	Completed technology	10,530
	Customer relationships	20,010
	Goodwill	26,453
	Other long term assets	885
	Accounts payable	(3,024		)
	Accrued liabilities	(5,172		)
	Deferred revenue	(319		)
	Other current liabilities	(388		)
	Other long-term liabilities	(8,232		)
	Total purchase price, net of cash acquired	$	59,005
	The Company recorded the assets and liabilities associated with the purchase of the Acquired assets at their fair values as of the acquisition date. The amounts recorded were as follows (in thousands):
	Accounts receivable	$	636
	Inventory	2,095
	Prepaid and other current assets	103
	Property, plant and equipment	534
	Completed technology	500
	Customer relationships	1,500
	Goodwill	7,076
	Debt	(902		)
	Accounts payable	(294		)
	Deferred revenue	(351		)
	Customer deposits	(1,249		)
	Other current liabilities	(322		)
	Total purchase price, net of cash acquired	$	9,326

Discontinued_Operations_Tables

Discontinued Operations (Tables)	6 Months Ended
	Mar. 31, 2014
Discontinued Operations and Disposal Groups [Abstract]	'
Schedules of Discontinued Operations	'
	Summarized results of the discontinued operation are as follows (in thousands):
		Three Months Ended					Six Months Ended
		March 31,					March 31,
		2014		2013			2014		2013
	Revenue	$	7,453	$	7,137		$	14,968	$	13,656
	Income from discontinued operations	$	1,825	$	2,198		$	4,309	$	3,602
	Income tax provision (benefit)	663		(456		)	1,570		(240		)
	Income from discontinued operations, net of tax	$	1,162	$	2,654		$	2,739	$	3,842
	The major classes of assets and liabilities of the discontinued operation as are follows (in thousands):
		March 31,		September 30,
		2014		2013
	Inventory	$	3,602	$	3,308
	Property, plant and equipment	315		364
	Goodwill	24,106		24,106
	Assets held for sale	$	28,023	$	27,778
	Deferred revenue	$	21	$	43
	Accrued warranty and retrofit costs	86		89
	Liabilities held for sale	$	107	$	132

Goodwill_and_Intangible_Assets1

Goodwill and Intangible Assets (Tables)	6 Months Ended
	Mar. 31, 2014
Goodwill and Intangible Assets Disclosure [Abstract]	'
Components of Goodwill by Business Segment	'
	The components of the Company’s goodwill, excluding amounts related to the discontinued operations, by business segment at March 31, 2014 are as follows (in thousands):
		Brooks			Brooks			Brooks			Other			Total
		Product			Global			Life Science
		Solutions			Services			Systems
	Gross goodwill at September 30, 2013	$	482,637		$	156,792		$	47,439		$	26,014		$	712,882
	Less: aggregate impairment charges recorded	(437,706		)	(151,238		)	—			(26,014		)	(614,958		)
	Goodwill, less accumulated impairments at September 30, 2013	44,931			5,554			47,439			—			97,924
	Adjustments during the six months ended March 31, 2014	—			—			(61		)	—			(61		)
	Goodwill, less accumulated impairments at March 31, 2014	$	44,931		$	5,554		$	47,378		$	—		$	97,863
Components of Identifiable Intangible Assets	'
	Components of the Company’s identifiable intangible assets, excluding amounts related to the discontinued operations, are as follows (in thousands):
		31-Mar-14									September 30, 2013
		Cost			Accumulated			Net Book			Cost			Accumulated			Net Book
					Amortization			Value						Amortization			Value
	Patents	$	7,808		$	7,248		$	560		$	7,808		$	7,196		$	612
	Completed technology	53,557			39,211			14,346			57,050			40,354			16,696
	Trademarks and trade names	3,496			3,496			—			3,564			3,554			10
	Customer relationships	67,134			26,916			40,218			66,687			23,917			42,770
		$	131,995		$	76,871		$	55,124		$	135,109		$	75,021		$	60,088

Earnings_per_Share_Tables

Earnings per Share (Tables)	6 Months Ended
	Mar. 31, 2014
Earnings Per Share [Abstract]	'
Reconciliation of Weighted Average Common Shares Outstanding for Purposes of Calculating Basic and Diluted Earnings Per Share	'
	Below is a reconciliation of weighted average common shares outstanding for purposes of calculating basic and diluted earnings per share (in thousands):
		Three months ended		Six months ended
		March 31,		March 31,
		2014	2013	2014	2013
	Weighted average common shares outstanding used in computing basic earnings per share	66,646	65,889	66,499	65,726
	Dilutive common stock options and restricted stock awards	859	—	884	—
	Weighted average common shares outstanding for purposes of computing diluted earnings per share	67,505	65,889	67,383	65,726

Segment_Information_Tables

Segment Information (Tables)	6 Months Ended
	Mar. 31, 2014
Segment Reporting [Abstract]	'
Financial Information for Business Segments	'
	Financial information for the Company’s business segments, excluding amounts related to the discontinued operations, is as follows (in thousands):
		Brooks			Brooks			Brooks			Total
		Product			Global			Life Science
		Solutions			Services			Systems
	Three months ended March 31, 2014
	Revenue
	Product	$	89,897		$	4,213		$	8,424		$	102,534
	Services	—			19,178			4,188			23,366
		$	89,897		$	23,391		$	12,612		$	125,900
	Gross profit	$	31,960		$	7,676		$	4,662		$	44,298
	Segment operating income (loss)	$	6,127		$	2,248		$	(3,565	)	$	4,810
	Three months ended March 31, 2013
	Revenue
	Product	$	78,563		$	3,731		$	6,358		$	88,652
	Services	—			18,073			2,757			20,830
		$	78,563		$	21,804		$	9,115		$	109,482
	Gross profit	$	24,313		$	6,359		$	2,411		$	33,083
	Segment operating income (loss)	$	1,464		$	1,799		$	(3,875	)	$	(612	)
	Six months ended March 31, 2014
	Revenue
	Product	$	171,453		$	7,652		$	16,559		$	195,664
	Services	—			39,058			8,250			47,308
		$	171,453		$	46,710		$	24,809		$	242,972
	Gross profit	$	60,461		$	15,501		$	9,227		$	85,189
	Segment operating income (loss)	$	10,455		$	5,091		$	(7,040	)	$	8,506
	Six months ended March 31 2013
	Revenue
	Product	$	134,990		$	7,236		$	17,454		$	159,680
	Services	—			35,509			5,799			41,308
		$	134,990		$	42,745		$	23,253		$	200,988
	Gross profit	$	39,293		$	11,366		$	8,705		$	59,364
	Segment operating income (loss)	$	(6,447	)	$	2,287		$	(3,897	)	$	(8,057	)
	Assets
	31-Mar-14	$	231,324		$	61,856		$	107,933		$	401,113
	September 30, 2013	$	226,759		$	59,762		$	105,221		$	391,742
Reconciliation of Reportable Segment Operating Income (Loss) to Corresponding Consolidated Amounts	'
	A reconciliation of the Company’s reportable segment operating income (loss) to the corresponding consolidated amounts for the three and six month periods ended March 31, 2014 and 2013 is as follows (in thousands):
		Three months ended						Six months ended
		March 31,						March 31,
		2014			2013			2014			2013
	Segment operating income (loss)	$	4,810		$	(612	)	$	8,506		$	(8,057	)
	Amortization of acquired intangible assets	1,460			1,413			2,916			2,856
	Restructuring and other charges	772			751			1,519			5,441
	Other unallocated corporate expenses	182			394			217			1,284
	Total operating income (loss)	$	2,396		$	(3,170	)	$	3,854		$	(17,638	)
Reconciliation of Reportable Segment Assets to Corresponding Consolidated Amounts	'
	A reconciliation of the Company’s reportable segment assets to the corresponding consolidated amounts as of March 31, 2014 and September 30, 2013 is as follows (in thousands):
		March 31,			September 30,
		2014			2013
	Segment assets	$	401,113		$	391,742
	Cash, cash equivalents, restricted cash and marketable securities	192,223			173,539
	Deferred tax assets	113,504			115,985
	Assets held for sale	28,023			27,778
	Equity method investments	30,342			25,687
	Other unallocated corporate net assets	2,016			2,032
	Total assets	$	767,221		$	736,763

Restructuring_and_Other_Charge1

Restructuring and Other Charges (Tables)	6 Months Ended
	Mar. 31, 2014
Restructuring and Related Activities [Abstract]	'
Activity Related to Restructuring Accruals	'
	The activity for the three and six months ended March 31, 2014 and 2013 related to the Company's restructuring-related accruals, excluding amounts related to the discontinued operations, is summarized below (in thousands):
		Activity — Three Months Ended March 31, 2014
		Balance at		Expense		Utilization			Balance at
		December 31,							March 31,
		2013							2014
	Facilities and other	$	57	$	7	$	(64	)	$	—
	Workforce-related	1,405		765		(618		)	1,552
		$	1,462	$	772	$	(682	)	$	1,552
		Activity - Three Months Ended March 31, 2013
		Balance at		Expense		Utilization			Balance at
		December 31,							March 31,
		2012							2013
	Facilities and other	$	265	$	112	$	(144	)	$	233
	Workforce-related	4,438		639		(2,746		)	2,331
		$	4,703	$	751	$	(2,890	)	$	2,564
		Activity — Six Months Ended March 31, 2014
		Balance at		Expense		Utilization			Balance at
		September 30,							March 31,
		2013							2014
	Facilities and other	$	155	$	13	$	(168	)	$	—
	Workforce-related	1,257		1,506		(1,211		)	1,552
		$	1,412	$	1,519	$	(1,379	)	$	1,552
		Activity — Six Months Ended March 31, 2013
		Balance at		Expense		Utilization			Balance at
		September 30,							March 31,
		2012							2013
	Facilities and other	$	—	$	690	$	(457	)	$	233
	Workforce-related	2,021		4,664		(4,354		)	2,331
		$	2,021	$	5,354	$	(4,811	)	$	2,564

Employee_Benefit_Plans_Tables

Employee Benefit Plans (Tables)	6 Months Ended
	Mar. 31, 2014
Compensation and Retirement Disclosure [Abstract]	'
Components of Net Pension Cost	'
	The components of the Company’s net pension cost for the three and six months ended March 31, 2014 and 2013 is as follows (in thousands):
		Three months ended						Six months ended
		March 31,						March 31,
		2014			2013			2014			2013
	Service cost	$	102		$	144		$	202		$	322
	Interest cost	39			35			78			80
	Amortization of losses	—			1			1			3
	Expected return on assets	(55		)	(58		)	(108		)	(135		)
	Net periodic pension cost	86			122			173			270
	Settlement loss	—			—			—			87
	Total pension cost	$	86		$	122		$	173		$	357

Capital_Lease_Obligation_Table

Capital Lease Obligation (Tables)	6 Months Ended
	Mar. 31, 2014
Leases [Abstract]	'
Schedule of Future Minimum Lease Payments	'
	The future minimum lease payments required under the capital lease and the present value of the net minimum lease payments, as of March 31, 2014, are as follows (in thousands):
	Year ended September 30,
	2014	$	441
	2015	881
	2016	881
	2017	881
	2018	6,901
	Total minimum lease payments	9,985
	Less amounts representing interest	1,448
	Total capital lease obligation	8,537
	Less current portion of capital lease obligation	881
	Long-term capital lease obligation	$	7,656

Other_Balance_Sheet_Informatio1

Other Balance Sheet Information (Tables)	6 Months Ended
	Mar. 31, 2014
Organization, Consolidation and Presentation of Financial Statements [Abstract]	'
Summary of Accounts Receivable	'
	The following is a summary of accounts receivable at March 31, 2014 and September 30, 2013 (in thousands):
		March 31,				September 30,
		2014				2013
	Accounts receivable	$	84,770			$	78,460
	Less allowance for doubtful accounts	(1,184		)		(863		)
	Less allowance for sales returns	(146		)		(114		)
		$	83,440			$	77,483
Summary of Inventories	'
	The following is a summary of inventories at March 31, 2014 and September 30, 2013, excluding amounts related to the discontinued operations (in thousands):
		March 31,				September 30,
		2014				2013
	Inventories
	Raw materials and purchased parts	$	59,844			$	57,678
	Work-in-process	17,083				19,991
	Finished goods	16,823				16,742
		$	93,750			$	94,411
Product Warranty and Retrofit Activity on Gross Basis	'
	Product warranty and retrofit activity on a gross basis for the three and six months ended March 31, 2014 and 2013, excluding amounts related to the discontinued operations, is as follows (in thousands):
	Activity - Three Months Ended March 31, 2014
	Balance at				Adjustments for				Accruals		Costs Incurred			Balance at
	December 31,				Acquisitions and Divestitures									March 31,
	2013													2014
	$	6,762			$	—			$	2,275	$	(2,718	)	$	6,319
	Activity - Three Months Ended March 31, 2013
	Balance at				Adjustments for				Accruals		Costs Incurred			Balance at
	December 31,				Acquisitions and Divestitures									March 31,
	2012													2013
	$	7,637			$	—			$	2,985	$	(2,987	)	$	7,635
	Activity - Six Months Ended March 31, 2014
	Balance at				Adjustments for				Accruals		Costs Incurred			Balance at
	September 30,				Acquisitions and Divestitures									March 31,
	2013													2014
	$	7,260			$	—			$	4,150	$	(5,091	)	$	6,319
	Activity - Six Months Ended March 31, 2013
	Balance at				Adjustments for				Accruals		Costs Incurred			Balance at
	September 30,				Acquisitions and Divestitures									March 31,
	2012													2013
	$	7,246			$	962			$	5,317	$	(5,890	)	$	7,635

Derivative_Instruments_Tables

Derivative Instruments (Tables)	6 Months Ended
	Mar. 31, 2014
Derivative Instruments and Hedging Activities Disclosure [Abstract]	'
Notional Amounts Outstanding under Foreign Currency Contracts	'
	The Company had the following notional amounts outstanding under foreign currency contracts that qualify for cash flow hedge accounting at March 31, 2014 (in thousands):
	Buy Currency		Notional Amount			Sell Currency	Maturity		Notional Amount			Fair Value of		Fair Value of
			of Buy Currency in U.S. Dollars						of Sell Currency			Assets		Liabilities
									in U.S. Dollars
	U.S. Dollar		$	2,037		Japanese Yen	Apr-14		$	1,946		$	91	$	—
	The Company had the following notional amounts outstanding under foreign currency contracts that do not qualify for hedge accounting at March 31, 2014 and September 30, 2013 (in thousands):
	March 31, 2014:
	Buy Currency		Notional Amount			Sell Currency	Maturity		Notional Amount			Fair Value of		Fair Value of
			of Buy Currency						of Sell Currency			Assets		Liabilities
									in U.S. Dollars
	U.S. Dollar		$	2,976		Japanese Yen	April to June 2014		$	2,973		$	3	$	—
	British Pound		2,470			Euro	April 2014		2,488			—		(18		)
	U.S. Dollar		698			Taiwan Dollar	April 2014		697			1		—
	Korean Won		605			U.S. Dollar	April 2014		602			3		—
	U.S. Dollar		428			Israeli Shekel	April 2014		431			—		(3		)
			$	7,177					$	7,191		$	7	$	(21	)
	September 30, 2013:
	Buy Currency		Notional Amount			Sell Currency	Maturity		Notional Amount			Fair Value of		Fair Value of
			of Buy Currency in U.S. Dollars						of Sell Currency			Assets		Liabilities
									in U.S. Dollars
	U.S. Dollar		$	2,770		Japanese Yen	October 2013 to December 2013		$	2,762		$	8	$	—
	Korean Won		686			U.S. Dollar	October 2013		688			—		2
	U.S. Dollar		301			Israeli Shekel	October 2013		304			—		3
	U.S. Dollar		231			Singapore Dollar	October 2013		231			—		—
			$	3,988					$	3,985		$	8	$	5
Schedule of Net Gains and Losses Realized on Derivative Instruments	'
	Net gains and losses recorded as a component of Other Income (Expense), net in the Consolidated Statements of Operations related to these contracts for the three and six month periods ended March 31, 2014 and 2013 is as follows (in thousands):
		Three Months Ended						Six Months Ended
		March 31,						March 31,
		2014			2013			2014			2013
	Realized gains (losses) on derivative instruments not designated as hedging instruments	$	(0.2	)	$	0.1		$	(0.1	)	$	0.1

Marketable_Securities_Tables

Marketable Securities (Tables)	6 Months Ended
	Mar. 31, 2014
Investments, Debt and Equity Securities [Abstract]	'
Summary of Marketable Securities Including Accrued Interest Receivable	'
	The following is a summary of marketable securities (included in short and long-term marketable securities in the Consolidated Balance Sheets), including accrued interest receivable, as of March 31, 2014 and September 30, 2013 (in thousands):
		Amortized		Gross		Gross			Fair Value
		Cost		Unrealized		Unrealized
				Gains		Losses
	March 31, 2014:
	U.S. Treasury securities and obligations of U.S. government agencies	$	15,876	$	3	$	(35	)	$	15,844
	Corporate securities	53,419		36		(30		)	53,425
	Mortgage-backed securities	1,035		31		—			1,066
	Other debt securities	899		—		—			899
	Municipal securities	23,882		11		(9		)	23,884
	Bank certificate of deposits	11,823		1		—			11,824
		$	106,934	$	82	$	(74	)	$	106,942
	September 30, 2013:
	U.S. Treasury securities and obligations of U.S. government agencies	$	19,528	$	6	$	(13	)	$	19,521
	Corporate securities	35,045		11		(47		)	35,009
	Mortgage-backed securities	1,093		25		(1		)	1,117
	Other debt securities	88		—		—			88
	Municipal securities	25,199		15		(7		)	25,207
	Bank certificate of deposits	9,451		—		(2		)	9,449
		$	90,404	$	57	$	(70	)	$	90,391
Fair Value of Marketable Securities by Contractual Maturity	'
	The fair value of the marketable securities at March 31, 2014 by contractual maturity, are shown below (in thousands). Expected maturities could differ from contractual maturities because the issuers of the securities may have the right to prepay obligations without prepayment penalties.
		Fair Value
	Due in one year or less	$	50,274
	Due after one year through five years	53,291
	Due after ten years	3,377
		$	106,942

Fair_Value_Measurements_Tables

Fair Value Measurements (Tables)	6 Months Ended
	Mar. 31, 2014
Fair Value Disclosures [Abstract]	'
Assets and Liabilities Measured at Fair Value on Recurring Basis	'
	Assets and liabilities of the Company measured at fair value on a recurring basis as of March 31, 2014 and September 30, 2013 are summarized as follows (in thousands):
				Fair Value Measurements at Reporting Date Using
	Description	March 31,		Quoted Prices in		Significant Other		Significant
		2014		Active Markets for		Observable Inputs		Unobservable Inputs
				Identical Assets		(Level 2)		(Level 3)
				(Level 1)
	Assets
	Cash equivalents	$	6,532	$	16	$	6,516	$	—
	Available-for-sale securities	106,942		—		106,942		—
	Foreign exchange contracts	98		—		98		—
	Total Assets	$	113,572	$	16	$	113,556	$	—
	Liabilities
	Foreign exchange contracts	$	21	$	—	$	21	$	—
				Fair Value Measurements at Reporting Date Using
	Description	September 30,		Quoted Prices in		Significant Other		Significant
		2013		Active Markets for		Observable Inputs		Unobservable Inputs
				Identical Assets		(Level 2)		(Level 3)
				(Level 1)
	Assets
	Cash equivalents	$	7,754	$	6,152	$	1,602	$	—
	Available-for-sale securities	90,391		2,199		88,192		—
	Foreign exchange contracts	31		—		31		—
	Total Assets	$	98,176	$	8,351	$	89,825	$	—
	Liabilities
	Foreign exchange contracts	$	5	$	—	$	5	$	—

StockBased_Compensation_Narrat

Stock-Based Compensation Narrative (Detail) (USD $)	3 Months Ended		6 Months Ended
	Mar. 31, 2014	Mar. 31, 2013	Mar. 31, 2014	Mar. 31, 2013
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'	'
Total compensation expense on awards	'	'	$6,516,000	$5,010,000
Closing stock price	$10.93	'	$10.93	'
Total intrinsic value of options exercised	'	19,000	'	19,000
Proceeds from stock options exercised	'	67,000	'	67,000
Stock purchase under employee stock purchase plan	115,132	115,751	115,132	115,751
Proceeds from issuance of shares under ESPP	1,000,000	1,000,000	1,000,000	1,000,000
Restricted Stock	'	'	'	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'	'
Restricted stocks granted	'	'	1,409,557	'
Fair value of restricted stock awards vested	1,800,000	3,100,000	4,900,000	6,000,000
Unrecognized compensation cost	15,700,000	'	15,700,000	'
Unrecognized compensation cost, estimated weighted average amortization period	'1 year 10 months	'	'	'
Restricted Stock | Senior Management	'	'	'	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'	'
Restricted stocks granted	'	'	1,409,557	1,224,000
Restricted Stock | Senior Management | Maximum	'	'	'	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'	'
Total compensation expense on awards	$19,200,000	$7,300,000	'	'
Restricted Stock | Senior Management | Awards Subject to Service Criteria	'	'	'	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'	'
Restricted stocks granted	'	'	601,432	546,625
Restricted Stock | Senior Management | Awards Subject to Performance Criteria	'	'	'	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'	'
Restricted stocks granted	'	'	808,125	677,375
Grants earned in period	'	'	'	460,615
Granville-Phillips [Member] | Restricted Stock	'	'	'	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'	'
Restricted stocks granted	'	'	8,500	29,380

StockBased_Compensation_StockB

Stock-Based Compensation Stock-Based Compensation Expense (Detail) (USD $)	3 Months Ended		6 Months Ended
In Thousands, unless otherwise specified	Mar. 31, 2014	Mar. 31, 2013	Mar. 31, 2014	Mar. 31, 2013
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'	'
Stock-based compensation	'	'	$6,516	$5,010
Continuing Operations	'	'	'	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'	'
Stock-based compensation	3,795	2,458	6,518	4,916
Continuing Operations | Restricted Stock	'	'	'	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'	'
Stock-based compensation	3,683	2,341	6,293	4,672
Continuing Operations | Employee Stock Purchase Plan	'	'	'	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'	'
Stock-based compensation	$112	$117	$225	$244

StockBased_Compensation_Stock_

Stock-Based Compensation Stock Option Activity (Detail) (USD $)	6 Months Ended
In Thousands, except Share data, unless otherwise specified	Mar. 31, 2014
Number of Stock Options	'
Options outstanding at beginning of period (shares)	15,540
Options outstanding at end of period (shares)	15,540
Vested at end of period (shares)	15,540
Options exercisable at end of period (shares)	15,540
Weighted-Average Remaining Contractual Term	'
Options outstanding at end of period	'4 months
Vested at end of period	'4 months
Options exercisable at end of period	'4 months
Weighted Average Exercise Price	'
Options outstanding at beginning of period (USD per share)	$15.86
Vested at end of period (USD per share)	$15.86
Options outstanding at end of year (USD per share)	$15.86
Options exercisable at end of period (USD per share)	$15.86
Options outstanding at end of period	$0
Vested at end of period	0
Options exercisable at end of period	$0

StockBased_Compensation_Status

Stock-Based Compensation Status of Restricted Stock Activity and Changes (Detail) (Restricted Stock, USD $)	6 Months Ended
	Mar. 31, 2014
Restricted Stock	'
Shares	'
Outstanding at Beginning of period (shares)	2,915,413
Awards granted (shares)	1,409,557
Awards vested (shares)	-522,023
Awards canceled (shares)	-767,962
Outstanding at End of period (shares)	3,034,985
Weighted Average Grant-Date Fair Value	'
Outstanding at beginning of period (USD per share)	$11.25
Awards granted (USD per share)	$9.46
Awards vested (USD per share)	$9.37
Awards canceled (USD per share)	$10.63
Outstanding at end of period (USD per share)	$10.90

Acquisition_Narrative_Detail

Acquisition Narrative (Detail) (USD $)	6 Months Ended		0 Months Ended	12 Months Ended		0 Months Ended	6 Months Ended
In Thousands, unless otherwise specified	Mar. 31, 2014	Mar. 31, 2013	Aug. 01, 2013	Sep. 30, 2013	Sep. 30, 2013	Oct. 29, 2012	Mar. 31, 2014	Mar. 31, 2014
			Matrical	Matrical	Matrical	Crossing Automation Inc	Crossing Automation Inc	Crossing Automation Inc
				Completed Technology	Customer Relationships		Completed Technology	Customer Relationships
Business Acquisition [Line Items]	'	'	'	'	'	'	'	'
Acquisition, net of cash acquired	$0	$59,005	$9,326	'	'	$59,005	'	'
Cash flow discount rate used to determine fair value attributed to completed technologies	'	'	18.00%	'	'	'	15.00%	'
Useful life of intangible assets acquired	'	'	'	'4 years 7 months	'7 years	'	'7 years 8 months	'8 years

Discontinued_Operations_Result

Discontinued Operations - Results of Operations (Details) (USD $)	0 Months Ended	3 Months Ended		6 Months Ended
	Mar. 19, 2014	Mar. 31, 2014	Mar. 31, 2013	Mar. 31, 2014	Mar. 31, 2013
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]	'	'	'	'	'
Income from discontinued operations, net of tax	'	$1,162,000	$2,654,000	$2,739,000	$3,842,000
Granville-Phillips [Member]	'	'	'	'	'
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]	'	'	'	'	'
Agreed upon sales price	87,000,000	'	'	'	'
Revenue	'	7,453,000	7,137,000	14,968,000	13,656,000
Income from discontinued operations	'	1,825,000	2,198,000	4,309,000	3,602,000
Income tax provision (benefit)	'	663,000	-456,000	1,570,000	-240,000
Income from discontinued operations, net of tax	'	$1,162,000	$2,654,000	$2,739,000	$3,842,000

Acquisition_Amounts_of_Assets_

Acquisition Amounts of Assets and Liabilities at Fair Value as of Acquisition Date (Detail) (USD $)	6 Months Ended			0 Months Ended			0 Months Ended
In Thousands, unless otherwise specified	Mar. 31, 2014	Mar. 31, 2013	Sep. 30, 2013	Aug. 01, 2013	Aug. 01, 2013	Aug. 01, 2013	Oct. 29, 2012	Oct. 29, 2012	Oct. 29, 2012
				Matrical	Matrical	Matrical	Crossing Automation Inc	Crossing Automation Inc	Crossing Automation Inc
					Completed Technology	Customer Relationships		Completed Technology	Customer Relationships
Business Acquisition [Line Items]	'	'	'	'	'	'	'	'	'
Accounts receivable	'	'	'	$636	'	'	$5,356	'	'
Inventory	'	'	'	2,095	'	'	8,668	'	'
Prepaid and other current assets	'	'	'	103	'	'	1,968	'	'
Property, plant and equipment	'	'	'	534	'	'	2,270	'	'
Finite-lived intangibles	'	'	'	'	500	1,500	'	10,530	20,010
Goodwill	97,863	'	97,924	7,076	'	'	26,453	'	'
Other long term assets	'	'	'	'	'	'	885	'	'
Debt	'	'	'	-902	'	'	'	'	'
Accounts payable	'	'	'	-294	'	'	-3,024	'	'
Accrued liabilities	'	'	'	'	'	'	-5,172	'	'
Deferred revenue	'	'	'	-351	'	'	-319	'	'
Customer deposits	'	'	'	-1,249	'	'	'	'	'
Other current liabilities	'	'	'	-322	'	'	-388	'	'
Other long-term liabilities	'	'	'	'	'	'	-8,232	'	'
Total purchase price, net of cash acquired	$0	$59,005	'	$9,326	'	'	$59,005	'	'

Discontinued_Operations_Schedu

Discontinued Operations - Schedule of Assets and Liabilities (Details) (Granville-Phillips [Member], USD $)	Mar. 31, 2014	Sep. 30, 2013
In Thousands, unless otherwise specified
Granville-Phillips [Member]	'	'
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]	'	'
Inventory	$3,602	$3,308
Property, plant and equipment	315	364
Goodwill	24,106	24,106
Assets held for sale	28,023	27,778
Deferred revenue	21	43
Accrued warranty and retrofit costs	86	89
Liabilities held for sale	$107	$132

Goodwill_and_Intangible_Assets2

Goodwill and Intangible Assets Components of Goodwill by Business Segment (Detail) (USD $)	6 Months Ended
In Thousands, unless otherwise specified	Mar. 31, 2014	Sep. 30, 2013
Goodwill [Line Items]	'	'
Gross goodwill at beginning of period	'	$712,882
Less: aggregate impairment charges recorded	'	-614,958
Goodwill [Roll Forward]	'	'
Goodwill, less accumulated impairments at beginning of period	97,924	'
Acquisitions and adjustments during the period	-61	'
Goodwill, less accumulated impairments at end of period	97,863	'
Brooks Product Solutions	'	'
Goodwill [Line Items]	'	'
Gross goodwill at beginning of period	'	482,637
Less: aggregate impairment charges recorded	'	-437,706
Goodwill [Roll Forward]	'	'
Goodwill, less accumulated impairments at beginning of period	44,931	'
Acquisitions and adjustments during the period	0	'
Goodwill, less accumulated impairments at end of period	44,931	'
Brooks Global Services	'	'
Goodwill [Line Items]	'	'
Gross goodwill at beginning of period	'	156,792
Less: aggregate impairment charges recorded	'	-151,238
Goodwill [Roll Forward]	'	'
Goodwill, less accumulated impairments at beginning of period	5,554	'
Acquisitions and adjustments during the period	0	'
Goodwill, less accumulated impairments at end of period	5,554	'
Brooks Life Science Systems	'	'
Goodwill [Line Items]	'	'
Gross goodwill at beginning of period	'	47,439
Less: aggregate impairment charges recorded	'	0
Goodwill [Roll Forward]	'	'
Goodwill, less accumulated impairments at beginning of period	47,439	'
Acquisitions and adjustments during the period	-61	'
Goodwill, less accumulated impairments at end of period	47,378	'
Other	'	'
Goodwill [Line Items]	'	'
Gross goodwill at beginning of period	'	26,014
Less: aggregate impairment charges recorded	'	-26,014
Goodwill [Roll Forward]	'	'
Goodwill, less accumulated impairments at beginning of period	0	'
Acquisitions and adjustments during the period	0	'
Goodwill, less accumulated impairments at end of period	$0	'

Goodwill_and_Intangible_Assets3

Goodwill and Intangible Assets Components of Identifiable Intangible Assets (Detail) (USD $)	Mar. 31, 2014	Sep. 30, 2013
In Thousands, unless otherwise specified
Finite-Lived Intangible Assets [Line Items]	'	'
Cost	$131,995	$135,109
Accumulated Amortization	76,871	75,021
Net Book Value	55,124	60,088
Patents	'	'
Finite-Lived Intangible Assets [Line Items]	'	'
Cost	7,808	7,808
Accumulated Amortization	7,248	7,196
Net Book Value	560	612
Completed Technology	'	'
Finite-Lived Intangible Assets [Line Items]	'	'
Cost	53,557	57,050
Accumulated Amortization	39,211	40,354
Net Book Value	14,346	16,696
Trademarks and Trade Names	'	'
Finite-Lived Intangible Assets [Line Items]	'	'
Cost	3,496	3,564
Accumulated Amortization	3,496	3,554
Net Book Value	0	10
Customer Relationships	'	'
Finite-Lived Intangible Assets [Line Items]	'	'
Cost	67,134	66,687
Accumulated Amortization	26,916	23,917
Net Book Value	$40,218	$42,770

Goodwill_and_Intangible_Assets4

Goodwill and Intangible Assets Narrative (Details) (USD $)	6 Months Ended		3 Months Ended	12 Months Ended
In Thousands, unless otherwise specified	Mar. 31, 2014	Mar. 31, 2013	Dec. 31, 2013	Sep. 30, 2013
			Celigo Cell Cytometer Product Line	Celigo Cell Cytometer Product Line
Goodwill [Line Items]	'	'	'	'
Impairment of assets	$398	$0	$400	$2,000

Income_Taxes_Narrative_Detail

Income Taxes Narrative (Detail) (USD $)	3 Months Ended		6 Months Ended
	Mar. 31, 2014	Mar. 31, 2013	Mar. 31, 2014	Mar. 31, 2013
Income Tax Contingency [Line Items]	'	'	'	'
Income tax provision (benefit)	$1,117,000	$327,000	$1,910,000	($3,559,000)
Minimum	'	'	'	'
Income Tax Contingency [Line Items]	'	'	'	'
Anticipated unrecognized tax benefit reduction during next twelve months	1,700,000	'	1,700,000	'
Maximum	'	'	'	'
Income Tax Contingency [Line Items]	'	'	'	'
Anticipated unrecognized tax benefit reduction during next twelve months	$2,800,000	'	$2,800,000	'

Earnings_per_Share_Reconciliat

Earnings per Share Reconciliation of Weighted Average Common Shares Outstanding for Purposes of Calculating Basic and Diluted Earnings Per Share (Detail)	3 Months Ended		6 Months Ended
In Thousands, unless otherwise specified	Mar. 31, 2014	Mar. 31, 2013	Mar. 31, 2014	Mar. 31, 2013
Earnings Per Share [Abstract]	'	'	'	'
Weighted average common shares outstanding used in computing basic earnings per share	66,646	65,889	66,499	65,726
Dilutive common stock options and restricted stock awards	859	0	884	0
Weighted average common shares outstanding for purposes of computing diluted earnings per share	67,505	65,889	67,383	65,726

Earnings_per_Share_Narrative_D

Earnings per Share Narrative (Detail)	3 Months Ended		6 Months Ended
In Thousands, unless otherwise specified	Mar. 31, 2014	Mar. 31, 2013	Mar. 31, 2014	Mar. 31, 2013
Stock Options	'	'	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'	'	'
Anti-dilutive securities excluded from computation of diluted earnings per share	16	34	16	65
Restricted Stock	'	'	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'	'	'
Anti-dilutive securities excluded from computation of diluted earnings per share	0	3,179	0	3,008

Segment_Information_Narrative_

Segment Information Narrative (Detail)	6 Months Ended
	Mar. 31, 2014
	segment
Segment Reporting [Abstract]	'
Number of reportable segments	3

Segment_Information_Financial_

Segment Information Financial Information for Business Segments (Detail) (USD $)	3 Months Ended		6 Months Ended
In Thousands, unless otherwise specified	Mar. 31, 2014	Mar. 31, 2013	Mar. 31, 2014	Mar. 31, 2013	Sep. 30, 2013
Revenues	'	'	'	'	'
Product	$102,534	$88,652	$195,664	$159,680	'
Services	23,366	20,830	47,308	41,308	'
Total revenues	125,900	109,482	242,972	200,988	'
Gross profit	44,298	33,083	85,189	59,364	'
Segment operating income (loss)	2,396	-3,170	3,854	-17,638	'
Total assets	767,221	'	767,221	'	736,763
Brooks Product Solutions	'	'	'	'	'
Revenues	'	'	'	'	'
Product	89,897	78,563	171,453	134,990	'
Services	0	0	0	0	'
Total revenues	89,897	78,563	171,453	134,990	'
Gross profit	31,960	24,313	60,461	39,293	'
Segment operating income (loss)	6,127	1,464	10,455	-6,447	'
Total assets	231,324	'	231,324	'	226,759
Brooks Global Services	'	'	'	'	'
Revenues	'	'	'	'	'
Product	4,213	3,731	7,652	7,236	'
Services	19,178	18,073	39,058	35,509	'
Total revenues	23,391	21,804	46,710	42,745	'
Gross profit	7,676	6,359	15,501	11,366	'
Segment operating income (loss)	2,248	1,799	5,091	2,287	'
Total assets	61,856	'	61,856	'	59,762
Brooks Life Science Systems	'	'	'	'	'
Revenues	'	'	'	'	'
Product	8,424	6,358	16,559	17,454	'
Services	4,188	2,757	8,250	5,799	'
Total revenues	12,612	9,115	24,809	23,253	'
Gross profit	4,662	2,411	9,227	8,705	'
Segment operating income (loss)	-3,565	-3,875	-7,040	-3,897	'
Total assets	107,933	'	107,933	'	105,221
Operating Segments	'	'	'	'	'
Revenues	'	'	'	'	'
Product	102,534	88,652	195,664	159,680	'
Services	23,366	20,830	47,308	41,308	'
Total revenues	125,900	109,482	242,972	200,988	'
Gross profit	44,298	33,083	85,189	59,364	'
Segment operating income (loss)	4,810	-612	8,506	-8,057	'
Total assets	$401,113	'	$401,113	'	$391,742

Segment_Information_Reconcilia

Segment Information Reconciliation of Reportable Segment Operating Income (Loss) to Corresponding Consolidated Amounts (Detail) (USD $)	3 Months Ended		6 Months Ended
In Thousands, unless otherwise specified	Mar. 31, 2014	Mar. 31, 2013	Mar. 31, 2014	Mar. 31, 2013
Segment Reporting, Reconciling Item for Operating Profit (Loss) from Segment to Consolidated [Line Items]	'	'	'	'
Other unallocated corporate expenses	$182	$394	$217	$1,284
Amortization of acquired intangible assets	1,460	1,413	2,916	2,856
Restructuring and other charges	772	751	1,519	5,441
Operating income (loss)	2,396	-3,170	3,854	-17,638
Operating Segments	'	'	'	'
Segment Reporting, Reconciling Item for Operating Profit (Loss) from Segment to Consolidated [Line Items]	'	'	'	'
Operating income (loss)	$4,810	($612)	$8,506	($8,057)

Segment_Information_Reconcilia1

Segment Information Reconciliation of Reportable Segment Assets to Corresponding Consolidated Amounts (Detail) (USD $)	Mar. 31, 2014	Sep. 30, 2013
In Thousands, unless otherwise specified
Segment Reporting, Asset Reconciling Item [Line Items]	'	'
Segment assets	$767,221	$736,763
Investments in cash, cash equivalents, restricted cash and marketable securities	192,223	173,539
Deferred tax assets	113,504	115,985
Assets held for sale	28,023	27,778
Investments in joint ventures	30,342	25,687
Other unallocated corporate net assets	2,016	2,032
Total assets	767,221	736,763
Operating Segments	'	'
Segment Reporting, Asset Reconciling Item [Line Items]	'	'
Segment assets	401,113	391,742
Total assets	$401,113	$391,742

Significant_Customers_Narrativ

Significant Customers Narrative (Detail)	3 Months Ended		6 Months Ended
	Mar. 31, 2014	Mar. 31, 2013	Mar. 31, 2014	Mar. 31, 2013
	customer
Risks and Uncertainties [Abstract]	'	'	'	'
Number of major customer by revenue	1	'	'	'
Percentage of revenues from one customer	10.00%	13.00%	12.00%	11.00%

Restructuring_and_Other_Charge2

Restructuring and Other Charges Narrative (Detail) (USD $)	6 Months Ended
In Millions, unless otherwise specified	Mar. 31, 2013	Mar. 31, 2014
		Polycold Manufacturing Operation
Restructuring Cost and Reserve [Line Items]	'	'
Expected severance cost	'	$1.10
Severance cost	'	0.8
Accelerated amortization of prior pension losses	$0.10	'

Restructuring_and_Other_Charge3

Restructuring and Other Charges Activity Related to Restructuring Accruals (Detail) (USD $)	3 Months Ended		6 Months Ended
In Thousands, unless otherwise specified	Mar. 31, 2014	Mar. 31, 2013	Mar. 31, 2014	Mar. 31, 2013
Restructuring Reserve [Roll Forward]	'	'	'	'
Beginning Balance	$1,462	$4,703	$1,412	$2,021
Expense	772	751	1,519	5,354
Utilization	-682	-2,890	-1,379	-4,811
Ending Balance	1,552	2,564	1,552	2,564
Facilities and Other	'	'	'	'
Restructuring Reserve [Roll Forward]	'	'	'	'
Beginning Balance	57	265	155	0
Expense	7	112	13	690
Utilization	-64	-144	-168	-457
Ending Balance	0	233	0	233
Workforce-related	'	'	'	'
Restructuring Reserve [Roll Forward]	'	'	'	'
Beginning Balance	1,405	4,438	1,257	2,021
Expense	765	639	1,506	4,664
Utilization	-618	-2,746	-1,211	-4,354
Ending Balance	$1,552	$2,331	$1,552	$2,331

Employee_Benefit_Plans_Narrati

Employee Benefit Plans Narrative (Detail) (USD $)	6 Months Ended	3 Months Ended
In Millions, unless otherwise specified	Mar. 31, 2013	Dec. 31, 2012
		Nexus Plan
Defined Benefit Plan Disclosure [Line Items]	'	'
Accelerated amortization of prior pension losses	$0.10	$0.10

Employee_Benefit_Plans_Compone

Employee Benefit Plans Components of Net Pension Cost (Detail) (USD $)	3 Months Ended		6 Months Ended
In Thousands, unless otherwise specified	Mar. 31, 2014	Mar. 31, 2013	Mar. 31, 2014	Mar. 31, 2013
Compensation and Retirement Disclosure [Abstract]	'	'	'	'
Service cost	$102	$144	$202	$322
Interest cost	39	35	78	80
Amortization of losses	0	1	1	3
Expected return on assets	-55	-58	-108	-135
Net periodic pension cost	86	122	173	270
Settlement loss	0	0	0	87
Total pension cost	$86	$122	$173	$357

Capital_Lease_Obligation_Narra

Capital Lease Obligation - Narrative (Details) (USD $)	Mar. 31, 2014
In Millions, unless otherwise specified
Building	'
Operating Leased Assets [Line Items]	'
Capital lease costs included in balance sheet as property, plant and equipment	$6.40
Land	'
Operating Leased Assets [Line Items]	'
Capital lease costs included in balance sheet as property, plant and equipment	$2.10

Capital_Lease_Obligation_Sched

Capital Lease Obligation - Schedule of Future Minimum Lease Payments (Details) (USD $)	Mar. 31, 2014	Sep. 30, 2013
In Thousands, unless otherwise specified
Leases [Abstract]	'	'
2014	$441	'
2015	881	'
2016	881	'
2017	881	'
2018	6,901	'
Total minimum lease payments	9,985	'
Less amounts representing interest	1,448	'
Total capital lease obligation	8,537	'
Less current portion of capital lease obligation	881	0
Long-term capital lease obligation	$7,656	$0

Other_Balance_Sheet_Informatio2

Other Balance Sheet Information Summary of Account Receivable (Detail) (USD $)	Mar. 31, 2014	Sep. 30, 2013
In Thousands, unless otherwise specified
Valuation and Qualifying Accounts Disclosure [Line Items]	'	'
Accounts receivable	$84,770	$78,460
Accounts receivable, net	83,440	77,483
Allowance for Doubtful Accounts	'	'
Valuation and Qualifying Accounts Disclosure [Line Items]	'	'
Less allowances	-1,184	-863
Allowance for Sales Returns	'	'
Valuation and Qualifying Accounts Disclosure [Line Items]	'	'
Less allowances	($146)	($114)

Other_Balance_Sheet_Informatio3

Other Balance Sheet Information Summary of Inventories (Detail) (USD $)	Mar. 31, 2014	Sep. 30, 2013
Organization, Consolidation and Presentation of Financial Statements [Abstract]	'	'
Raw materials and purchased parts	$59,844,000	$57,678,000
Work-in-process	17,083,000	19,991,000
Finished goods	16,823,000	16,742,000
Inventory, net	93,750,000	94,411,000
Reserves for excess and obsolete inventory	$24,100,000	'

Other_Balance_Sheet_Informatio4

Other Balance Sheet Information Product Warranty and Retrofit Activity on Gross Basis (Detail) (USD $)	3 Months Ended		6 Months Ended
In Thousands, unless otherwise specified	Mar. 31, 2014	Mar. 31, 2013	Mar. 31, 2014	Mar. 31, 2013
Organization, Consolidation and Presentation of Financial Statements [Abstract]	'	'	'	'
Beginning Balance	$6,762	$7,637	$7,260	$7,246
Adjustments for acquisitions and divestitures	0	0	0	962
Accruals	2,275	2,985	4,150	5,317
Costs incurred	-2,718	-2,987	-5,091	-5,890
Ending Balance	$6,319	$7,635	$6,319	$7,635

Equity_Method_Investments_Narr

Equity Method Investments Narrative (Detail) (USD $)	3 Months Ended		6 Months Ended
	Mar. 31, 2014	Mar. 31, 2013	Mar. 31, 2014	Mar. 31, 2013	Sep. 30, 2013
Schedule of Equity Method Investments [Line Items]	'	'	'	'	'
Equity in earnings (losses) of joint ventures	$510,000	($10,000)	$1,259,000	($16,000)	'
Equity investment in joint ventures	30,342,000	'	30,342,000	'	25,687,000
BioCision, LLC	'	'	'	'	'
Schedule of Equity Method Investments [Line Items]	'	'	'	'	'
Joint venture interest, percentage	22.00%	'	22.00%	'	'
Investment cost	4,000,000	'	4,000,000	'	'
ULVAC Cryogenics, Inc.	'	'	'	'	'
Schedule of Equity Method Investments [Line Items]	'	'	'	'	'
Joint venture interest, percentage	50.00%	'	50.00%	'	'
Equity in earnings (losses) of joint ventures	500,000	0	1,200,000	100,000	'
Equity investment in joint ventures	23,400,000	'	23,400,000	'	'
Management fee payments received	100,000	'	300,000	200,000	'
Charges incurred from related parties	0	100,000	100,000	400,000	'
Accounts payable for unpaid products and services	27,000	'	27,000	'	0
Yaskawa Brooks Automation, Inc.	'	'	'	'	'
Schedule of Equity Method Investments [Line Items]	'	'	'	'	'
Joint venture interest, percentage	50.00%	'	50.00%	'	'
Equity in earnings (losses) of joint ventures	35,000	6,000	17,000	-78,000	'
Equity investment in joint ventures	2,900,000	'	2,900,000	'	'
Charges incurred from related parties	200,000	200,000	300,000	300,000	'
Accounts payable for unpaid products and services	0	'	0	'	47,000
Revenues earned from joint ventures	2,100,000	1,300,000	2,800,000	2,900,000	'
Due from joint venture	$2,100,000	'	$2,100,000	'	$2,300,000

Derivative_Instruments_Realize

Derivative Instruments - Realized Gains (Losses) on Derivative Instruments (Details) (USD $)	3 Months Ended		6 Months Ended
In Thousands, unless otherwise specified	Mar. 31, 2014	Mar. 31, 2013	Mar. 31, 2014	Mar. 31, 2013
Derivative Instruments and Hedging Activities Disclosure [Abstract]	'	'	'	'
Realized gains (losses) on derivative instruments not designated as hedging instruments	$0	$0	$0	$0

Derivative_Instruments_Notiona

Derivative Instruments - Notional Amounts Outstanding under Foreign Currency Contracts (Detail) (Foreign Exchange Contract, USD $)	Mar. 31, 2014	Sep. 30, 2013
In Thousands, unless otherwise specified
Designated as Hedging Instrument | Buy Currency, U.S. Dollar; Sell Currency, Japanese Yen	'	'
Derivative [Line Items]	'	'
Fair Value of Assets	$91	'
Fair Value of Liabilities	0	'
Designated as Hedging Instrument | Long | Buy Currency, U.S. Dollar; Sell Currency, Japanese Yen	'	'
Derivative [Line Items]	'	'
Notional Amount	2,037	'
Designated as Hedging Instrument | Short | Buy Currency, U.S. Dollar; Sell Currency, Japanese Yen	'	'
Derivative [Line Items]	'	'
Notional Amount	1,946	'
Not Designated as Hedging Instrument	'	'
Derivative [Line Items]	'	'
Fair Value of Assets	7	8
Fair Value of Liabilities	-21	-5
Not Designated as Hedging Instrument | Buy Currency, U.S. Dollar; Sell Currency, Japanese Yen	'	'
Derivative [Line Items]	'	'
Fair Value of Assets	3	8
Fair Value of Liabilities	0	0
Not Designated as Hedging Instrument | Buy Currency, British Pound; Sell Currency, Euro	'	'
Derivative [Line Items]	'	'
Fair Value of Assets	0	'
Fair Value of Liabilities	-18	'
Not Designated as Hedging Instrument | Buy Currency, U.S. Dollar; Sell Currency, Taiwan Dollar	'	'
Derivative [Line Items]	'	'
Fair Value of Assets	1	'
Fair Value of Liabilities	0	'
Not Designated as Hedging Instrument | Buy Currency, Korean Won; Sell Currency, US Dollar	'	'
Derivative [Line Items]	'	'
Fair Value of Assets	3	0
Fair Value of Liabilities	0	-2
Not Designated as Hedging Instrument | Buy Currency, U.S. Dollar; Sell Currency, Israeli Shekel	'	'
Derivative [Line Items]	'	'
Fair Value of Assets	0	0
Fair Value of Liabilities	-3	-3
Not Designated as Hedging Instrument | Buy Currency, U.S. Dollar; Sell Currency, Singapore Dollar	'	'
Derivative [Line Items]	'	'
Fair Value of Assets	'	0
Fair Value of Liabilities	'	0
Not Designated as Hedging Instrument | Long	'	'
Derivative [Line Items]	'	'
Notional Amount	7,177	3,988
Not Designated as Hedging Instrument | Long | Buy Currency, U.S. Dollar; Sell Currency, Japanese Yen	'	'
Derivative [Line Items]	'	'
Notional Amount	2,976	2,770
Not Designated as Hedging Instrument | Long | Buy Currency, British Pound; Sell Currency, Euro	'	'
Derivative [Line Items]	'	'
Notional Amount	2,470	'
Not Designated as Hedging Instrument | Long | Buy Currency, U.S. Dollar; Sell Currency, Taiwan Dollar	'	'
Derivative [Line Items]	'	'
Notional Amount	698	'
Not Designated as Hedging Instrument | Long | Buy Currency, Korean Won; Sell Currency, US Dollar	'	'
Derivative [Line Items]	'	'
Notional Amount	605	686
Not Designated as Hedging Instrument | Long | Buy Currency, U.S. Dollar; Sell Currency, Israeli Shekel	'	'
Derivative [Line Items]	'	'
Notional Amount	428	301
Not Designated as Hedging Instrument | Long | Buy Currency, U.S. Dollar; Sell Currency, Singapore Dollar	'	'
Derivative [Line Items]	'	'
Notional Amount	'	231
Not Designated as Hedging Instrument | Short	'	'
Derivative [Line Items]	'	'
Notional Amount	7,191	3,985
Not Designated as Hedging Instrument | Short | Buy Currency, U.S. Dollar; Sell Currency, Japanese Yen	'	'
Derivative [Line Items]	'	'
Notional Amount	2,973	2,762
Not Designated as Hedging Instrument | Short | Buy Currency, British Pound; Sell Currency, Euro	'	'
Derivative [Line Items]	'	'
Notional Amount	2,488	'
Not Designated as Hedging Instrument | Short | Buy Currency, U.S. Dollar; Sell Currency, Taiwan Dollar	'	'
Derivative [Line Items]	'	'
Notional Amount	697	'
Not Designated as Hedging Instrument | Short | Buy Currency, Korean Won; Sell Currency, US Dollar	'	'
Derivative [Line Items]	'	'
Notional Amount	602	688
Not Designated as Hedging Instrument | Short | Buy Currency, U.S. Dollar; Sell Currency, Israeli Shekel	'	'
Derivative [Line Items]	'	'
Notional Amount	431	304
Not Designated as Hedging Instrument | Short | Buy Currency, U.S. Dollar; Sell Currency, Singapore Dollar	'	'
Derivative [Line Items]	'	'
Notional Amount	'	$231

Marketable_Securities_Summary_

Marketable Securities Summary of Marketable Securities Including Accrued Interest Receivable (Detail) (USD $)	3 Months Ended
In Thousands, unless otherwise specified	Mar. 31, 2014	Sep. 30, 2013
Schedule of Available-for-sale Securities [Line Items]	'	'
Amortized Cost	$106,934	$90,404
Gross Unrealized Gains	82	57
Gross Unrealized Losses	-74	-70
Fair Value	106,942	90,391
U.S. Treasury securities and obligations of U.S. government agencies	'	'
Schedule of Available-for-sale Securities [Line Items]	'	'
Amortized Cost	15,876	19,528
Gross Unrealized Gains	3	6
Gross Unrealized Losses	-35	-13
Fair Value	15,844	19,521
Corporate securities	'	'
Schedule of Available-for-sale Securities [Line Items]	'	'
Amortized Cost	53,419	35,045
Gross Unrealized Gains	36	11
Gross Unrealized Losses	-30	-47
Fair Value	53,425	35,009
Mortgage-backed securities	'	'
Schedule of Available-for-sale Securities [Line Items]	'	'
Amortized Cost	1,035	1,093
Gross Unrealized Gains	31	25
Gross Unrealized Losses	0	-1
Fair Value	1,066	1,117
Other debt securities	'	'
Schedule of Available-for-sale Securities [Line Items]	'	'
Amortized Cost	899	88
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Fair Value	899	88
Municipal securities	'	'
Schedule of Available-for-sale Securities [Line Items]	'	'
Amortized Cost	23,882	25,199
Gross Unrealized Gains	11	15
Gross Unrealized Losses	-9	-7
Fair Value	23,884	25,207
Bank certificate of deposits	'	'
Schedule of Available-for-sale Securities [Line Items]	'	'
Amortized Cost	11,823	9,451
Gross Unrealized Gains	1	0
Gross Unrealized Losses	0	-2
Fair Value	$11,824	$9,449

Marketable_Securities_Fair_Val

Marketable Securities Fair Value of Marketable Securities by Contractual Maturity (Detail) (USD $)	Mar. 31, 2014	Sep. 30, 2013
In Thousands, unless otherwise specified
Investments, Debt and Equity Securities [Abstract]	'	'
Due in one year or less	$50,274	'
Due after one year through five years	53,291	'
Due after ten years	3,377	'
Fair Value	$106,942	$90,391

Fair_Value_Measurements_Narrat

Fair Value Measurements Narrative (Detail) (USD $)	Mar. 31, 2014	Sep. 30, 2013
In Thousands, unless otherwise specified
Fair Value Assets And Liabilities Measured On Recurring Basis [Line Items]	'	'
Available-for-sale securities	$106,942	$90,391
Fair Value, Measurements, Recurring	'	'
Fair Value Assets And Liabilities Measured On Recurring Basis [Line Items]	'	'
Available-for-sale securities	106,942	90,391
Cash and Cash Equivalents, Fair Value Disclosure	6,532	7,754
Fair Value, Measurements, Recurring | Quoted Prices in Active Markets for Identical Assets (Level 1)	'	'
Fair Value Assets And Liabilities Measured On Recurring Basis [Line Items]	'	'
Available-for-sale securities	0	2,199
Cash and Cash Equivalents, Fair Value Disclosure	16	6,152
Fair Value, Measurements, Recurring | Significant Other Observable Inputs (Level 2)	'	'
Fair Value Assets And Liabilities Measured On Recurring Basis [Line Items]	'	'
Available-for-sale securities	106,942	88,192
Cash and Cash Equivalents, Fair Value Disclosure	$6,516	$1,602

Fair_Value_Measurements_Assets

Fair Value Measurements Assets and Liabilities Measured at Fair Value on Recurring Basis (Detail) (USD $)	Mar. 31, 2014	Sep. 30, 2013
In Thousands, unless otherwise specified
Assets	'	'
Available-for-sale securities	$106,942	$90,391
Fair Value, Measurements, Recurring	'	'
Assets	'	'
Cash Equivalents	6,532	7,754
Available-for-sale securities	106,942	90,391
Foreign exchange contracts	98	31
Total Assets	113,572	98,176
Liabilities	'	'
Foreign exchange contracts	'	5
Quoted Prices in Active Markets for Identical Assets (Level 1) | Fair Value, Measurements, Recurring	'	'
Assets	'	'
Cash Equivalents	16	6,152
Available-for-sale securities	0	2,199
Foreign exchange contracts	0	0
Total Assets	16	8,351
Liabilities	'	'
Foreign exchange contracts	0	0
Significant Other Observable Inputs (Level 2) | Fair Value, Measurements, Recurring	'	'
Assets	'	'
Cash Equivalents	6,516	1,602
Available-for-sale securities	106,942	88,192
Foreign exchange contracts	98	31
Total Assets	113,556	89,825
Liabilities	'	'
Foreign exchange contracts	$21	$5

Commitments_and_Contingencies_

Commitments and Contingencies - Additional Information (Details) (USD $)	Mar. 31, 2014
In Millions, unless otherwise specified
Commitments and Contingencies Disclosure [Abstract]	'
Outstanding letters of credit	$20.50

Subsequent_Events_Detail

Subsequent Events (Detail) (USD $)	3 Months Ended		6 Months Ended		0 Months Ended
In Millions, except Per Share data, unless otherwise specified	Mar. 31, 2014	Mar. 31, 2013	Mar. 31, 2014	Mar. 31, 2013	8-May-14	Apr. 30, 2014
					Subsequent Event	Subsequent Event
Subsequent Event [Line Items]	'	'	'	'	'	'
Purchase price	'	'	'	'	'	$31
Liabilities incurred	'	'	'	'	'	$16
Cash dividend declared (USD per share)	$0.08	$0.08	$0.16	$0.16	$0.08	'
Cash dividend declared, payment date	'	'	'	'	27-Jun-14	'
Cash dividend declared, record date	'	'	'	'	6-Jun-14	'