Condensed Consolidated Statements of Operations (Unaudited) (USD $) In Thousands, except Per Share data, unless otherwise specified	3 Months Ended		6 Months Ended
	Mar. 31, 2013	Mar. 31, 2012	Mar. 31, 2013	Mar. 31, 2012
Income Statement [Abstract]
Revenues, net of returns and allowances	$ 8,118	$ 21,566	$ 17,475	$ 46,294
Cost of sales	5,665	17,518	13,644	35,045
Gross profit	2,453	4,048	3,831	11,249
Selling, general and administrative	3,968	6,046	8,238	12,338
Restructuring and impairment charges	0	688	697	688
Research and development	1,946	3,299	3,108	6,052
Operating loss	(3,461)	(5,985)	(8,212)	(7,829)
Interest and other income, net	39	39	44	126
Loss before income taxes	(3,422)	(5,946)	(8,168)	(7,703)
Income tax benefit	(800)	(220)	(1,280)	(540)
Net loss	(2,622)	(5,726)	(6,888)	(7,163)
Add: Net Loss Attributable to noncontrolling interest	530	647	603	1,208
Net loss attributable to Amtech Systems, Inc.	$ (2,092)	$ (5,079)	$ (6,285)	$ (5,955)
Loss Per Share:
Basic loss per share attributable to Amtech shareholders (dollars per share)	$ (0.22)	$ (0.54)	$ (0.66)	$ (0.63)
Weighted average shares outstanding (in shares)	9,539	9,479	9,516	9,462
Diluted loss per share attributable to Amtech shareholders (dollars per share)	$ (0.22)	$ (0.54)	$ (0.66)	$ (0.63)
Weighted average shares outstanding (in shares)	9,539	9,479	9,516	9,462