CONSOLIDATED BALANCE SHEETS (USD $) In Thousands, unless otherwise specified	Dec. 31, 2011	Sep. 30, 2011
Current assets
Cash and cash equivalents	$ 49,213	$ 58,833
Restricted cash	863	1,293
Marketable securities	79,465	65,695
Accounts receivable, net	73,684	76,701
Inventories, net	102,612	107,654
Prepaid expenses and other current assets	10,467	10,348
Total current assets	316,304	320,524
Property, plant and equipment, net	67,349	68,596
Long-term marketable securities	65,826	81,290
Goodwill	88,440	84,727
Intangible assets, net	45,547	44,314
Equity investment in joint ventures	35,357	34,612
Other assets	2,981	2,557
Total assets	621,804	636,620
Current liabilities
Accounts payable	34,257	40,199
Deferred revenue	11,980	14,073
Accrued warranty and retrofit costs	7,293	7,438
Accrued compensation and benefits	13,150	17,288
Accrued restructuring costs	321	293
Accrued income taxes payable	3,387	4,015
Accrued expenses and other current liabilities	14,040	12,433
Total current liabilities	84,428	95,739
Income taxes payable	11,706	11,728
Long-term pension liability	7,239	7,161
Other long-term liabilities	3,677	3,394
Total liabilities	107,050	118,022
Contingencies (Note 16)
Equity
Preferred stock, $0.01 par value, 1,000,000 shares authorized, no shares issued and outstanding
Common stock, $0.01 par value, 125,000,000 shares authorized, 79,716,314 shares issued and 66,254,445 shares outstanding at December 31, 2011, 79,737,189 shares issued and 66,275,320 shares outstanding at September 30, 2011	797	797
Additional paid-in capital	1,810,829	1,809,287
Accumulated other comprehensive income	16,273	19,480
Treasury stock at cost, 13,461,869 shares at December 31, 2011 and September 30, 2011	(200,956)	(200,956)
Accumulated deficit	(1,112,786)	(1,110,599)
Total Brooks Automation, Inc. stockholders' equity	514,157	518,009
Noncontrolling interest in subsidiaries	597	589
Total equity	514,754	518,598
Total liabilities and equity	$ 621,804	$ 636,620