Condensed Consolidated Statements of Operations (Unaudited) (USD $) In Thousands, except Per Share data, unless otherwise specified	3 Months Ended
	Dec. 31, 2013	Dec. 31, 2012
Income Statement [Abstract]
Revenues, net of returns and allowances	$ 14,772	$ 9,357
Cost of sales	10,237	7,979
Gross profit	4,535	1,378
Selling, general and administrative	4,124	4,272
Restructuring charges	0	697
Research and development	889	1,161
Operating loss	(478)	(4,752)
Interest and other income, net	106	4
Loss before income taxes	(372)	(4,748)
Income tax provision (benefit)	560	(480)
Net loss	(932)	(4,268)
Add: Net loss attributable to noncontrolling interest	138	74
Net loss attributable to Amtech Systems, Inc.	$ (794)	$ (4,194)
Loss Per Share:
Basic loss per share attributable to Amtech shareholders (dollars per share)	$ (0.08)	$ (0.44)
Weighted average shares outstanding (in shares)	9,560	9,494
Diluted loss per share attributable to Amtech shareholders (dollars per share)	$ (0.08)	$ (0.44)
Weighted average shares outstanding (in shares)	9,560	9,494