Goodwill and Intangible Assets - Goodwill Roll Forward (Details) - USD ($) $ in Thousands	12 Months Ended
	Sep. 30, 2017	Sep. 30, 2016
Goodwill [Roll Forward]
Goodwill, net of accumulated impairments, beginning balance	$ 202,138	$ 121,408
Acquisitions and adjustments	31,500	80,730
Goodwill, net of accumulated impairments, ending balance	233,638	202,138
Brooks Semiconductor Solutions Group
Goodwill [Roll Forward]
Goodwill, net of accumulated impairments, beginning balance	66,837	65,783
Acquisitions and adjustments	(19)	1,054
Goodwill, net of accumulated impairments, ending balance	66,818	66,837
Brooks Life Science Systems
Goodwill [Roll Forward]
Goodwill, net of accumulated impairments, beginning balance	135,301	55,625
Acquisitions and adjustments	31,519	79,676
Goodwill, net of accumulated impairments, ending balance	$ 166,820	$ 135,301