CONSOLIDATED BALANCE SHEETS (USD $) In Thousands, unless otherwise specified	Mar. 31, 2013	Sep. 30, 2012
Current assets
Cash and cash equivalents	$ 60,121	$ 54,639
Restricted cash	0	763
Marketable securities	46,242	85,646
Accounts receivable, net	73,545	78,855
Inventories	96,601	102,985
Deferred tax assets	18,460	15,531
Prepaid expenses and other current assets	11,773	9,070
Total current assets	306,742	347,489
Property, plant and equipment, net	58,874	64,478
Long-term marketable securities	39,211	59,946
Long-term deferred tax assets	99,551	104,626
Goodwill	114,893	88,440
Intangible assets, net	64,576	39,400
Equity investment in joint ventures	28,425	31,428
Other assets	9,490	6,153
Total assets	721,762	741,960
Current liabilities
Accounts payable	28,658	28,988
Deferred revenue	13,613	9,986
Accrued warranty and retrofit costs	7,725	7,329
Accrued compensation and benefits	12,409	14,118
Accrued restructuring costs	2,580	2,098
Accrued income taxes payable	390	1,699
Accrued expenses and other current liabilities	16,138	16,973
Total current liabilities	81,513	81,191
Income taxes payable	7,945	6,356
Long-term pension liability	1,411	1,688
Other long-term liabilities	3,618	3,424
Total liabilities	94,487	92,659
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, 79,952,679 shares issued and 66,490,810 shares outstanding at March 31, 2013, 79,790,557 shares issued and 66,328,688 shares outstanding at September 30, 2012	799	798
Additional paid-in capital	1,822,102	1,817,706
Accumulated other comprehensive income	17,512	23,642
Treasury stock at cost, 13,461,869 shares	(200,956)	(200,956)
Accumulated deficit	(1,012,861)	(992,524)
Total Brooks Automation, Inc. stockholders' equity	626,596	648,666
Noncontrolling interest in subsidiaries	679	635
Total equity	627,275	649,301
Total liabilities and equity	$ 721,762	$ 741,960