Condensed Consolidated Balance Sheets (USD $) In Thousands, unless otherwise specified	Jun. 30, 2012	Sep. 30, 2011
Current Assets
Cash and cash equivalents	$ 42,326	$ 67,382
Restricted cash	3,330	6,571
Accounts receivable
Trade (less allowance for doubtful accounts of $455 and $246 at June 30, 2012 and September 30, 2011, respectively)	16,608	14,447
Unbilled and other	13,331	30,822
Inventories	33,075	37,162
Deferred income taxes	9,520	9,560
Prepaid income taxes	970	4,260
Other	2,969	4,647
Total current assets	122,129	174,851
Property, Plant and Equipment - Net	11,980	12,680
Intangible Assets - Net	4,221	5,021
Goodwill	13,006	13,313
Total Assets	151,336	205,865
Current Liabilities
Accounts payable	6,024	8,928
Accrued compensation and related taxes	5,680	10,686
Accrued warranty expense	3,271	2,265
Deferred profit	11,396	27,608
Customer deposits	3,447	7,862
Other accrued liabilities	4,354	6,775
Income taxes payable	7,680	16,670
Total current liabilities	41,852	80,794
Income Taxes Payable Long-term	2,390	2,630
Deferred Income Taxes Long-term	40	110
Total liabilities	44,282	83,534
Commitments and Contingencies
Stockholders' Equity
Preferred stock; 100,000,000 shares authorized; none issued	0	0
Common stock; $0.01 par value; 100,000,000 shares authorized; shares issued and outstanding: 9,479,007 and 9,431,393 at June 30, 2012 and September 30, 2011, respectively	95	94
Additional paid-in capital	84,550	83,207
Accumulated other comprehensive (loss)	(7,458)	(2,078)
Retained Earnings	26,176	35,096
Total Amtech Systems Inc. stockholders' equity	103,363	116,319
Noncontrolling interest	3,691	6,012
Total Equity	107,054	122,331
Total Liabilities and Stockholders' Equity	$ 151,336	$ 205,865