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Consolidated Statements of Cash Flows (USD $)
 12 Months Ended 125 Months Ended
Sep. 30, 2013
Sep. 30, 2012
Sep. 30, 2013
CASH FLOWS FROM OPERATING ACTIVITIES OF CONTINUING OPERATIONS:      
Net Loss $ (31,703,433) $ (22,110,723) $ (185,356,438)
Net loss attributable to noncontrolling interests 560,144 984,795 19,379,429
NET LOSS ATTRIBUTABLE TO ARROWHEAD (31,143,289) (21,125,928) (165,977,009)
(Income) loss from discontinued operations 354 80 42,838,408
Realized and unrealized (gain) loss on investments   58,091 (762,954)
Charge for bad debt allowance   2,497,300 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 1,079,377 1,282,853
Stock issued for professional services     741,632
Change in value of derivatives 5,300,389 (386,892) 2,018,985
Contingent consideration – fair value adjustments 1,421,652   1,421,652
Purchased in-process research and development     15,851,555
Stock-based compensation 1,536,271 1,241,404 15,117,739
Depreciation and amortization 1,751,412 1,748,975 9,160,698
Amortization (accretion) of note discounts, net 128,406 9,390 129,858
Gain on sale of stock in subsidiary     (2,292,800)
Noncash impairment expense 2,315,721 1,642,775 3,958,496
Equity in income (loss) of unconsolidated affiliates   240,154 963,407
Noncontrolling interest (560,144) (984,795) (19,379,429)
Trade receivables (65,625) 162,855 34,415
Other receivables 1,080 (938,179) (2,542,062)
Prepaid expenses 44,713 (338,531) (436,386)
Other current assets (1,811) (30,600) (165,566)
Accounts payable 321,647 291,876 819,957
Accrued expenses 27,920 186,369 748,829
Other liabilities (187,910) 882,296 942,251
NET CASH USED IN OPERATING ACTIVITIES OF CONTINUING OPERATIONS (19,032,826) (15,340,090) (94,910,622)
CASH FLOWS FROM INVESTING ACTIVITIES OF CONTINUING OPERATIONS:      
Purchases of property and equipment (296,880) (479,710) (4,342,189)
Proceeds from sale of investments 1,419,079 509,009 4,732,688
Proceeds from sale of fixed assets 89,505 290,312 522,192
Purchase of marketable securities (10,732,571)   (29,308,486)
Proceeds from sale of marketable securities     18,888,265
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 (9,520,867) 440,644 (12,850,593)
CASH FLOWS FROM FINANCING ACTIVITIES OF CONTINUING OPERATIONS:      
Principal payments on capital lease obligations (214,801) (196,606) (411,407)
Proceeds from issuance of common stock, preferred stock and warrants, net 44,506,004 10,958,231 150,759,015
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 44,291,203 10,769,625 173,766,175
Cash flows from discontinued operations:      
Operating cash flows (354) (280) (46,004,141)
Investing cash flows     790,625
Financing cash flows     (1,677,000)
Net cash used in discontinued operations: (354) (280) (46,890,516)
NET INCREASE (DECREASE) IN CASH 15,737,156 (4,130,101) 19,114,444
CASH AT BEGINNING OF PERIOD 3,377,288 7,507,389  
CASH AT END OF PERIOD 19,114,444 3,377,288 19,114,444
Supplementary disclosures:      
Interest paid 42,044 42,269 322,732
Taxes paid     $ 742,500