CONSOLIDATED BALANCE SHEETS (USD $) In Thousands, unless otherwise specified	Mar. 31, 2012	Sep. 30, 2011
Current assets
Cash and cash equivalents	$ 81,155	$ 58,833
Restricted cash	817	1,293
Marketable securities	71,057	65,695
Accounts receivable, net	80,492	76,701
Inventories, net	105,065	107,654
Prepaid expenses and other current assets	10,051	10,348
Total current assets	348,637	320,524
Property, plant and equipment, net	66,676	68,596
Long-term marketable securities	52,059	81,290
Goodwill	88,440	84,727
Intangible assets, net	43,881	44,314
Equity investment in joint ventures	33,924	34,612
Other assets	3,059	2,557
Total assets	636,676	636,620
Current liabilities
Accounts payable	46,048	40,199
Deferred revenue	10,595	14,073
Accrued warranty and retrofit costs	7,281	7,438
Accrued compensation and benefits	12,820	17,288
Accrued restructuring costs	120	293
Accrued income taxes payable	3,273	4,015
Accrued expenses and other current liabilities	13,329	12,433
Total current liabilities	93,466	95,739
Income taxes payable	10,318	11,728
Long-term pension liability	7,209	7,161
Other long-term liabilities	3,401	3,394
Total liabilities	114,394	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, 79,778,340 shares issued and 66,316,471 shares outstanding at March 31, 2012, 79,737,189 shares issued and 66,275,320 shares outstanding at September 30, 2011	798	797
Additional paid-in capital	1,813,848	1,809,287
Accumulated other comprehensive income	16,710	19,480
Treasury stock at cost, 13,461,869 shares at March 31, 2012 and September 30, 2011	(200,956)	(200,956)
Accumulated deficit	(1,108,720)	(1,110,599)
Total Brooks Automation, Inc. stockholders' equity	521,680	518,009
Noncontrolling interest in subsidiaries	602	589
Total equity	522,282	518,598
Total liabilities and equity	$ 636,676	$ 636,620