CONSOLIDATED BALANCE SHEETS (USD $) In Thousands, unless otherwise specified	Dec. 31, 2012	Sep. 30, 2012
Current assets
Cash and cash equivalents	$ 54,923	$ 54,639
Restricted cash	768	763
Marketable securities	48,070	85,646
Accounts receivable, net	63,832	78,855
Inventories	105,123	102,985
Deferred tax assets	18,134	15,531
Prepaid expenses and other current assets	9,879	9,070
Total current assets	300,729	347,489
Property, plant and equipment, net	65,006	64,478
Long-term marketable securities	38,996	59,946
Long-term deferred tax assets	101,135	104,626
Goodwill	114,043	88,440
Intangible assets, net	67,439	39,400
Equity investment in joint ventures	30,437	31,428
Other assets	7,044	6,153
Total assets	724,829	741,960
Current liabilities
Accounts payable	21,199	28,988
Deferred revenue	8,927	9,986
Accrued warranty and retrofit costs	7,724	7,329
Accrued compensation and benefits	13,425	14,118
Accrued restructuring costs	4,793	2,098
Accrued income taxes payable	891	1,699
Accrued expenses and other current liabilities	17,248	16,973
Total current liabilities	74,207	81,191
Income taxes payable	8,065	6,356
Long-term pension liability	1,415	1,688
Other long-term liabilities	3,853	3,424
Total liabilities	87,540	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, 79,807,305 shares issued and 66,345,436 shares outstanding at December 31, 2012, 79,790,557 shares issued and 66,328,688 shares outstanding at September 30, 2012	798	798
Additional paid-in capital	1,819,402	1,817,706
Accumulated other comprehensive income	24,420	23,642
Treasury stock at cost, 13,461,869 shares	(200,956)	(200,956)
Accumulated deficit	(1,007,027)	(992,524)
Total Brooks Automation, Inc. stockholders' equity	636,637	648,666
Noncontrolling interest in subsidiaries	652	635
Total equity	637,289	649,301
Total liabilities and equity	$ 724,829	$ 741,960