Income Taxes (Details) - USD ($) $ in Thousands	12 Months Ended
	Jun. 30, 2015	Jun. 30, 2014	Jun. 30, 2013
Reconciliation of the Company's expected tax benefit, as computed by applying the U.S. federal corporate tax rate to loss before the benefit for income taxes, and actual tax
U.S. federal corporate tax rate (as a percent)	34.00%	34.00%	34.00%
Loss before income tax expense	$ (60,739)	$ (71,364)	$ (72,811)
Expected tax benefit at 34%	(20,651)	(24,264)	(24,756)
Permanent differences	2,766	1,953	1,540
State tax benefit net of federal benefit	(3,252)	(4,062)	(3,921)
Increase in valuation allowance, net	27,940	26,011	25,624
Federal research credit	(1,407)	(1,002)	(2,260)
Federal orphan drug credit	(5,471)
Expired loss and credit carryforwards	75	$ 1,364	$ 3,773
Federal
Net operating loss carryforwards
Operating loss carryforward	249,300
Operating loss carryforward related to deductions from the exercise of stock options	25,600
State
Net operating loss carryforwards
Operating loss carryforward	87,100
Operating loss carryforward related to deductions from the exercise of stock options	$ 22,200