Segment Information - Financial Information for Business Segments (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016	Sep. 30, 2016
Revenue
Products	$ 141,957	$ 111,596	$ 396,684	$ 302,238
Services	39,760	35,938	114,321	100,532
Total revenue	181,717	147,534	511,005	402,770
Gross profit	71,572	54,163	193,039	141,517
Segment operating income (loss)	18,770	8,494	46,732	(6,165)
Total assets	746,771		746,771		$ 685,905
Brooks Semiconductor Solutions Group
Revenue
Products	124,681	99,254	349,710	268,671
Services	20,280	19,179	56,532	57,657
Total revenue	144,961	118,433	406,242	326,328
Gross profit	58,083	42,904	154,877	114,506
Brooks Life Science Systems
Revenue
Products	17,276	12,342	46,974	33,567
Services	19,480	16,759	57,789	42,875
Total revenue	36,756	29,101	104,763	76,442
Gross profit	13,489	11,259	38,162	27,011
Operating Segments
Revenue
Segment operating income (loss)	27,322	12,383	66,097	15,162
Depreciation expense	2,326	2,466	7,055	5,827
Total assets	592,996		592,996		565,452
Operating Segments | Brooks Semiconductor Solutions Group
Revenue
Segment operating income (loss)	26,188	13,119	63,562	22,717
Depreciation expense	1,192	1,448	3,786	3,375
Total assets	330,746		330,746		317,717
Operating Segments | Brooks Life Science Systems
Revenue
Segment operating income (loss)	1,134	(736)	2,535	(7,555)
Depreciation expense	1,134	$ 1,018	3,269	$ 2,452
Total assets	$ 262,250		$ 262,250		$ 247,735