Condensed Consolidated Statements of Operations (Unaudited) (USD $) In Thousands, except Per Share data, unless otherwise specified	3 Months Ended
	Dec. 31, 2012	Dec. 31, 2011
Income Statement [Abstract]
Revenues, net of returns and allowances	$ 9,357	$ 24,728
Cost of sales	7,979	17,527
Gross profit	1,378	7,201
Selling, general and administrative	4,272	6,292
Restructuring charges	697	0
Research and development	1,161	2,753
Operating loss	(4,752)	(1,844)
Interest and other income, net	4	87
Loss before income taxes	(4,748)	(1,757)
Income tax benefit	(480)	(320)
Net loss	(4,268)	(1,437)
Add: Net Loss Attributable to noncontrolling interest	74	561
Net loss attributable to Amtech Systems, Inc.	$ (4,194)	$ (876)
Loss Per Share:
Basic loss per share attributable to Amtech shareholders (dollars per share)	$ (0.44)	$ (0.09)
Weighted average shares outstanding (in shares)	9,494	9,446
Diluted loss per share attributable to Amtech shareholders (dollars per share)	$ (0.44)	$ (0.09)
Weighted average shares outstanding (in shares)	9,494	9,446