Goodwill and Intangible Assets - Goodwill Roll Forward (Details) $ in Thousands	9 Months Ended
	Jun. 30, 2017 USD ($)
Goodwill [Roll Forward]
Goodwill, net of accumulated impairments, beginning balance	$ 202,138
Acquisitions and adjustments	8,471
Goodwill, net of accumulated impairments, ending balance	210,609
Brooks Semiconductor Solutions Group
Goodwill [Roll Forward]
Goodwill, net of accumulated impairments, beginning balance	66,837
Acquisitions and adjustments	(56)
Goodwill, net of accumulated impairments, ending balance	66,781
Brooks Life Science Systems
Goodwill [Roll Forward]
Goodwill, net of accumulated impairments, beginning balance	135,301
Acquisitions and adjustments	8,527
Goodwill, net of accumulated impairments, ending balance	$ 143,828