Condensed Consolidated Statements of Operations (Unaudited) (USD $) In Thousands, except Per Share data, unless otherwise specified	3 Months Ended		9 Months Ended
	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2013	Jun. 30, 2012
Income Statement [Abstract]
Revenues, net of returns and allowances	$ 10,398	$ 24,300	$ 27,873	$ 70,594
Cost of sales	8,648	17,146	22,639	50,861
Write-down of inventory	4,427	2,350	4,080	3,680
Gross profit	(2,677)	4,804	1,154	16,053
Selling, general and administrative	5,443	6,360	13,682	18,698
Restructuring and impairment charges	182	0	879	688
Research and development	1,947	3,694	5,055	9,746
Operating loss	(10,249)	(5,250)	(18,462)	(13,079)
Interest and other income, net	143	69	187	195
Loss before income taxes	(10,106)	(5,181)	(18,275)	(12,884)
Income tax benefit	2,560	(1,110)	1,280	(1,650)
Net loss	(12,666)	(4,071)	(19,555)	(11,234)
Add: Net Loss Attributable to noncontrolling interest	565	1,106	1,169	2,314
Net loss attributable to Amtech Systems, Inc.	$ (12,101)	$ (2,965)	$ (18,386)	$ (8,920)
Loss Per Share:
Basic loss per share attributable to Amtech shareholders (dollars per share)	$ (1.27)	$ (0.31)	$ (1.93)	$ (0.94)
Weighted average shares outstanding (in shares)	9,539	9,479	9,524	9,468
Diluted loss per share attributable to Amtech shareholders (dollars per share)	$ (1.27)	$ (0.31)	$ (1.93)	$ (0.94)
Weighted average shares outstanding (in shares)	9,539	9,479	9,524	9,468