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Consolidated Statements of Cash Flows (USD $)
 9 Months Ended 122 Months Ended
Jun. 30, 2013
Jun. 30, 2012
Jun. 30, 2013
CASH FLOWS FROM OPERATING ACTIVITIES:      
Net income (loss) $ (17,898,373) $ (16,509,974) $ (171,551,378)
Net (income) loss attributable to noncontrolling interests 447,268 697,727 19,266,553
NET LOSS ATTRIBUTABLE TO ARROWHEAD (17,451,105) (15,812,247) (152,284,825)
(Income) loss from discontinued operations 354 25 42,838,408
Realized and unrealized (gain) loss on investments   58,091 (762,954)
Charge for bad debt allowance     2,497,300
(Gain) loss from sale of subsidiary     (306,344)
(Gain) loss on purchase of Roche Madison   (1,576,107) (1,576,107)
(Gain) loss on disposal of fixed assets 76,388 909,761 1,282,853
Stock issued for professional services     741,632
Change in value of derivatives (215,620) (226,339) (3,497,024)
Purchased in-process research and development     15,851,555
Stock-based compensation 1,114,375 837,188 14,695,843
Depreciation and amortization 1,352,448 1,301,806 8,761,734
Amortization (accretion) of note discounts, net 82,341 (20,633) 83,793
Gain on sale of stock in subsidiary       (2,292,800)
Noncash impairment expense 2,315,721 1,455,775 3,958,496
Equity in income (loss) of unconsolidated affiliates   205,361 963,407
Noncontrolling interest (447,268) (697,727) (19,266,553)
Receivables 9,375 169,150 109,415
Other receivables 1,080 1,173,523 (2,542,062)
Prepaid expenses (441,373) (152,782) (922,472)
Other current assets (1,813) (30,286) (165,568)
Accounts payable 183,959 408,263 682,269
Accrued expenses 95,132 514,117 816,041
Other liabilities (313,354) 730,771 816,807
NET CASH USED IN OPERATING ACTIVITIES OF CONTINUING OPERATIONS (13,639,360) (10,752,290) (89,517,156)
CASH FLOWS FROM INVESTING ACTIVITIES OF CONTINUING OPERATIONS:      
Purchase of property and equipment (191,656) (392,799) (4,236,965)
Proceeds from sale of investments   509,009 3,313,609
Proceeds from sale of fixed assets (89,505) 25,037 522,192
Purchase of marketable securities (4,058,003)   (22,633,918)
Proceeds from sale of marketable securities 1,160,181   20,048,446
Cash transferred in acquisitions/divestitures   121,033 (1,579,365)
Purchase of MASA Energy, LLC     (250,000)
Minority equity investment     (2,000,000)
Cash paid for interest in Insert     (10,150,000)
Cash obtained from interest in Insert     10,529,594
Proceeds from sale of subsidiaries     359,375
Payment for patents     (303,440)
Restricted cash     50,773
NET CASH PROVIDED BY (USED IN) INVESTING ACTIVITIES OF CONTINUING OPERATIONS (2,999,973) 262,280 (6,329,699)
CASH FLOWS FROM FINANCING ACTIVITIES OF CONTINUING OPERATIONS:      
Principal payments on capital leases (160,495) (143,905) (357,101)
Proceeds from issuance of common stock and warrants, net 42,448,824 5,401,392 148,701,835
Proceeds from issuance of Calando debt     2,516,467
Proceeds from sale of stock in subsidiary   8,000 20,902,100
NET CASH PROVIDED BY FINANCING ACTIVITIES OF CONTINUING OPERATIONS 42,288,329 5,265,487 171,763,301
Cash flows from discontinued operations:      
Operating cash flows (354) (225) (46,004,141)
Investing cash flows     790,625
Financing cash flows     (1,677,000)
Net cash provided by (used in) discontinued operations: (354) (225) (46,890,516)
NET INCREASE (DECREASE) IN CASH 25,648,642 (5,224,748) 29,025,930
CASH AT BEGINNING OF PERIOD 3,377,288 7,507,389  
CASH AT END OF PERIOD 29,025,930 2,282,641 29,025,930
Supplementary disclosures:      
Interest paid 32,139 34,758 312,827
Taxes paid     $ 742,500