Array 10-K15 Aug 142014 FY Annual reportFinancial data

Company Profile

Document_and_Entity_Informatio

Document and Entity Information (USD $)	12 Months Ended
Document and Entity Information (USD $)	Jun. 30, 2014	Jul. 31, 2014	Dec. 31, 2013
Document and Entity Information	'	'	'
Entity Registrant Name	'ARRAY BIOPHARMA INC	'	'
Entity Central Index Key	'0001100412	'	'
Current Fiscal Year End Date	'--06-30	'	'
Entity Filer Category	'Accelerated Filer	'	'
Document Type	'10-K	'	'
Document Period End Date	30-Jun-14	'	'
Document Fiscal Year Focus	'2014	'	'
Document Fiscal Period Focus	'FY	'	'
Amendment Flag	'false	'	'
Entity Current Reporting Status	'Yes	'	'
Entity Common Stock, Shares Outstanding	'	131,822,939	'
Entity Well-known Seasoned Issuer	'No	'	'
Entity Voluntary Filers	'No	'	'
Entity Public Float	'	'	$616,083,027

Balance_Sheets

Balance Sheets (USD $)	Jun. 30, 2014	Jun. 30, 2013
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013
Current assets	'	'
Cash and cash equivalents	$68,591	$60,736
Marketable securities	42,407	47,505
Accounts receivable	5,429	9,595
Prepaid expenses and other current assets	5,249	3,473
Total current assets	121,676	121,309
Long-term assets	'	'
Marketable securities	640	465
Property and equipment, net	8,157	10,049
Other long-term assets	8,580	4,165
Total long-term assets	17,377	14,679
Total assets	139,053	135,988
Current liabilities	'	'
Accounts payable	6,953	5,396
Accrued outsourcing costs	10,040	5,576
Accrued compensation and benefits	8,209	9,481
Other accrued expenses	1,444	1,135
Co-development liability	16,155	10,990
Deferred rent	3,739	3,646
Deferred revenue	6,193	14,353
Total current liabilities	52,733	50,577
Long-term liabilities	'	'
Deferred rent	4,096	7,834
Deferred revenue	3,353	0
Long-term debt, net	103,952	99,021
Other long-term liabilities	640	465
Total long-term liabilities	112,041	107,320
Total liabilities	164,774	157,897
Commitments and contingencies	'	'
Stockholders' deficit	'	'
Preferred stock, $0.001 par value; 10,000,000 shares authorized, no shares issued and outstanding	0	0
Common stock, $0.001 par value; 220,000,000 shares authorized; 131,817,422 and 116,878,021 shares issued and outstanding as of June 30, 2014 and 2013, respectively	132	117
Additional paid-in capital	652,696	571,270
Warrants	39,385	39,385
Accumulated other comprehensive income (loss)	2	-2
Accumulated deficit	-717,936	-632,679
Total stockholders' deficit	-25,721	-21,909
Total liabilities and stockholders' deficit	$139,053	$135,988

Balance_Sheets_Parenthetical

Balance Sheets (Parenthetical) (USD $)	Jun. 30, 2014	Jun. 30, 2013
Statement of Financial Position [Abstract]	'	'
Common stock, par value (in dollars per share)	$0.00	$0.00
Common stock, shares authorized	220,000,000	220,000,000
Common stock, shares issued	131,817,422	116,878,021
Common stock, shares outstanding	131,817,422	116,878,021
Preferred stock, par value (in dollars per share)	$0.00	$0.00
Preferred stock, shares authorized	10,000,000	10,000,000
Preferred stock, shares issued	0	0
Preferred stock, shares outstanding	0	0

Statements_of_Operations_and_C

Statements of Operations and Comprehensive Loss (USD $)	12 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2012
Revenue	'	'	'
License and milestone revenue	$25,111	$56,726	$71,249
Collaboration revenue	16,967	12,854	13,886
Total revenue	42,078	69,580	85,135
Operating expenses	'	'	'
Cost of partnered programs	45,965	30,078	24,261
Research and development for proprietary programs	49,824	59,420	56,719
General and administrative	21,907	19,624	15,202
Total operating expenses	117,696	109,122	96,182
Loss from operations	-75,618	-39,542	-11,047
Other income (expense)	'	'	'
Loss on prepayment of long-term debt, net	0	-11,197	-942
Interest income	77	55	32
Interest expense	-9,716	-11,258	-11,624
Total other expense, net	-9,639	-22,400	-12,534
Net loss	-85,257	-61,942	-23,581
Change in unrealized gains and losses on marketable securities	4	-1	-4
Comprehensive loss	($85,253)	($61,943)	($23,585)
Weighted average shares outstanding b basic and diluted	123,403	107,794	70,619
Net loss per share b basic and diluted	($0.69)	($0.57)	($0.33)

Statements_of_Stockholders_Def

Statements of Stockholders' Deficit (USD $)	Total	Preferred Stock	Common Stock	Additional Paid-in Capital	Warrants	Accumulated Other Comprehensive Income (Loss)	Accumulated Deficit
In Thousands, unless otherwise specified	Total	Preferred Stock	Common Stock	Additional Paid-in Capital	Warrants	Accumulated Other Comprehensive Income (Loss)	Accumulated Deficit
Balance at Jun. 30, 2011	($130,858)	$30,000	$57	$346,853	$39,385	$3	($547,156)
Balance (in shares) at Jun. 30, 2011	'	10	57,020	'	'	'	'
Increase (Decrease) in Stockholders' Equity	'	'	'	'	'	'	'
Stock Issued During Period, Value, Share-based Compensation, Net of Forfeitures	1,169	'	1	1,168	'	'	'
Stock Issued During Period, Shares, Share-based Compensation, Net of Forfeitures	'	'	581	'	'	'	'
Share-based compensation expense	2,351	'	'	2,351	'	'	'
Issuance of common stock, net of offering costs	63,148	'	26	63,122	'	'	'
Issuance of common stock, net of offering costs (in shares)	'	'	25,936	'	'	'	'
Conversion of preferred stock to common	0	-21,946	7	21,939	'	'	'
Conversion of preferred stock to common (in shares)	'	-7	7,414	'	'	'	'
Payment of employee bonus with stock	1,969	'	1	1,968	'	'	'
Payment of employee bonus with stock (in shares)	'	'	1,113	'	'	'	'
Change in unrealized gain or loss on marketable securities	-4	'	'	'	'	-4	'
Net loss	-23,581	'	'	'	'	'	-23,581
Balance at Jun. 30, 2012	-85,806	8,054	92	437,401	39,385	-1	-570,737
Balance (in shares) at Jun. 30, 2012	'	3	92,064	'	'	'	'
Increase (Decrease) in Stockholders' Equity	'	'	'	'	'	'	'
Stock Issued During Period, Value, Share-based Compensation, Net of Forfeitures	2,120	'	1	2,119	'	'	'
Stock Issued During Period, Shares, Share-based Compensation, Net of Forfeitures	'	'	900	'	'	'	'
Share-based compensation expense	3,449	'	'	3,449	'	'	'
Issuance of common stock, net of offering costs	70,896	'	21	70,875	'	'	'
Issuance of common stock, net of offering costs (in shares)	'	'	20,700	'	'	'	'
Conversion of preferred stock to common	0	-8,054	3	8,051	'	'	'
Conversion of preferred stock to common (in shares)	'	-3	2,721	'	'	'	'
Payment of employee bonus with stock	2,857	'	'	2,857	'	'	'
Payment of employee bonus with stock (in shares)	'	'	493	'	'	'	'
Issuance of convertible senior notes, equity portion, net of offering costs	46,518	'	'	46,518	'	'	'
Change in unrealized gain or loss on marketable securities	-1	'	'	'	'	-1	'
Net loss	-61,942	'	'	'	'	'	-61,942
Balance at Jun. 30, 2013	-21,909	0	117	571,270	39,385	-2	-632,679
Balance (in shares) at Jun. 30, 2013	'	0	116,878	'	'	'	'
Increase (Decrease) in Stockholders' Equity	'	'	'	'	'	'	'
Stock Issued During Period, Value, Share-based Compensation, Net of Forfeitures	3,693	'	1	3,692	'	'	'
Stock Issued During Period, Shares, Share-based Compensation, Net of Forfeitures	'	'	1,132	'	'	'	'
Share-based compensation expense	4,331	'	'	4,331	'	'	'
Issuance of common stock, net of offering costs	73,448	'	14	73,434	'	'	'
Issuance of common stock, net of offering costs (in shares)	'	'	13,807	'	'	'	'
Change in unrealized gain or loss on marketable securities	4	'	'	'	'	4	'
Net loss	-85,257	'	'	'	'	'	-85,257
Offering costs for convertible senior notes, equity portion	-31	'	'	-31	'	'	'
Balance at Jun. 30, 2014	($25,721)	$0	$132	$652,696	$39,385	$2	($717,936)
Balance (in shares) at Jun. 30, 2014	'	0	131,817	'	'	'	'

Statements_of_Cash_Flows

Statements of Cash Flows (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2012
Cash flows from operating activities	'	'	'
Net loss	($85,257)	($61,942)	($23,581)
Adjustments to reconcile net loss to net cash used in operating activities:	'	'	'
Depreciation and amortization expense	4,506	4,350	5,076
Non-cash interest expense	5,258	4,476	4,643
Loss on prepayment of long-term debt	0	11,197	942
Share-based compensation expense	4,331	3,449	2,351
Payment of employee bonus with stock	0	2,857	1,969
Non-cash license revenue	-4,500	0	0
Changes in operating assets and liabilities:	'	'	'
Accounts receivable	4,166	-8,520	1,157
Prepaid expenses and other assets	-1,961	-746	1,044
Accounts payable and other accrued expenses	1,866	-1,324	1,084
Accrued outsourcing costs	4,464	182	146
Accrued compensation and benefits	-1,272	1,951	1,099
Co-development liability	5,165	1,812	5,581
Deferred rent	-3,645	-3,489	-3,332
Deferred revenue	-4,807	-41,214	-31,613
Other liabilities	4	-106	-112
Net cash used in operating activities	-71,682	-87,067	-33,546
Cash flows from investing activities	'	'	'
Purchases of property and equipment	-2,614	-2,340	-1,437
Purchases of marketable securities	-95,602	-110,723	-51,339
Proceeds from sales and maturities of marketable securities	100,698	96,701	34,055
Net cash provided by (used in) investing activities	2,482	-16,362	-18,721
Cash flows from financing activities	'	'	'
Proceeds from the issuance of convertible senior notes	0	132,250	0
Payments of long-term debt principal	0	-92,712	-4,350
Proceeds from the issuance of common stock	75,000	75,555	67,145
Proceeds from employee stock purchases and options exercised	3,693	2,120	1,169
Payment of debt issuance costs	-86	-4,188	0
Payment of stock offering costs	-1,552	-4,659	-3,997
Net cash provided by financing activities	77,055	108,366	59,967
Net increase in cash and cash equivalents	7,855	4,937	7,700
Cash and cash equivalents at beginning of period	60,736	55,799	48,099
Cash and cash equivalents at end of period	68,591	60,736	55,799
Supplemental disclosure of cash flow information	'	'	'
Cash paid for interest	$4,349	$6,564	$7,008

OVERVIEW_AND_BASIS_OF_PRESENTA

OVERVIEW AND BASIS OF PRESENTATION

12 Months Ended

Jun. 30, 2014

Organization, Consolidation and Presentation of Financial Statements [Abstract]

OVERVIEW AND BASIS OF PRESENTATION

Organization

Array BioPharma Inc. (also referred to as "Array," "we," "us," or "our"), incorporated in Delaware on February 6, 1998, is a biopharmaceutical company focused on the discovery, development and commercialization of targeted small molecule drugs to treat patients afflicted with cancer.

Basis of Presentation

The accompanying financial statements have been prepared in accordance with U.S. generally accepted accounting principles (“U.S. GAAP”) and include all adjustments necessary for the fair presentation of our financial position, results of operations and cash flows for the periods presented. Our management performed an evaluation of our activities through the date of filing of this Annual Report on Form 10-K, and concluded that there are no subsequent events, except as disclosed in Note 13 to these financial statements.

Use of Estimates

The preparation of financial statements in conformity with U.S. GAAP requires our management to make estimates and assumptions that affect the reported amounts of assets, liabilities, revenue and expenses, and related disclosure of contingent assets and liabilities. Management bases its estimates on our historical experience and on various other assumptions that we believe are reasonable under the circumstances. These estimates are the basis for our judgments about the carrying values of assets and liabilities, which in turn may impact our reported revenue and expenses. Our actual results could differ significantly from these estimates under different assumptions or conditions.

We believe our financial statements are most significantly impacted by the following accounting estimates and judgments: (i) the identification of deliverables under collaboration and license agreements involving multiple elements and determining whether such deliverables are separable from other aspects of the contractual relationship; (ii) estimating the selling price of deliverables for the purpose of allocating arrangement consideration for revenue recognition; (iii) estimating the periods over which the allocated consideration for deliverables is recognized; (iv) estimating accrued outsourcing costs for clinical trials and preclinical testing; (v) estimating the fair value of non-marketable equity received from licensing transactions; and (vi) determination of fair value of the debt component for our convertible senior notes exclusive of the conversion feature.

Liquidity

We have incurred operating losses and an accumulated deficit as a result of ongoing research and development spending since inception. As of June 30, 2014, we had an accumulated deficit of $717.9 million. We had net losses of $85.3 million, $61.9 million, and $23.6 million for the fiscal years ended June 30, 2014, 2013 and 2012, respectively.

We have historically funded our operations from up-front fees and license and milestone payments received under our drug collaboration and license agreements, the sale of equity securities, and debt provided by convertible debt and other credit facilities. We believe that our cash, cash equivalents and marketable securities as of June 30, 2014 will enable us to continue to fund operations in the normal course of business for at least the next 12 months. Until we can generate sufficient levels of cash from current operations, which we do not expect to achieve in the foreseeable future, and because sufficient funds may not be available to us when needed from existing collaborations, we expect that we will be required to continue to fund our operations in part through the sale of debt or equity securities and through licensing select programs that include up-front and/or milestone payments.

Our ability to successfully raise sufficient funds through the sale of debt or equity securities or from debt financing from lenders when needed is subject to many risks and uncertainties and, even if we are successful, future equity issuances would result in dilution to our existing stockholders. We also may not successfully consummate new collaboration and license agreements that provide for up-front fees or milestone payments, or we may not earn milestone payments under such agreements when anticipated, or at all. Our ability to realize milestone or royalty payments under existing agreements and to enter into new arrangements that generate additional revenue through up-front fees and milestone or royalty payments is subject to a number of risks, many of which are beyond our control. For example, although following the recently announced transaction by Novartis to exchange certain assets with GlaxoSmithKline, Novartis has indicated that it will continue to honor its obligations under its License Agreement with Array for the development of binimetinib, including the three Phase 3 trials currently underway; however, the transaction could affect the program in ways we may not anticipate. For example, the program could revert to Array, and development efforts, and any potential future milestone or royalty revenue, may be affected by this transaction.

In addition, our assessment of our future need for funding and our ability to continue to fund our operations is a forward-looking statement that is based on assumptions that may prove to be wrong and that involve substantial risks and uncertainties.

If we are unable to generate enough revenue from our existing or new collaboration and license agreements when needed or to secure additional sources of funding, it may be necessary to significantly reduce the current rate of spending through further reductions in staff and delaying, scaling back, or stopping certain research and development programs, including more costly Phase 2 and Phase 3 clinical trials on our wholly-owned or co-development programs as these programs progress into later stage development. Insufficient liquidity may also require us to relinquish greater rights to product candidates at an earlier stage of development or on less favorable terms to us and our stockholders than we would otherwise choose in order to obtain up-front license fees needed to fund operations. These events could prevent us from successfully executing our operating plan and, in the future, could raise substantial doubt about our ability to continue as a going concern. Further, as discussed in Note 5 – Long-term Debt, if at any time our balance of total cash, cash equivalents and marketable securities at Comerica Bank and approved outside accounts falls below $22 million, we must maintain a balance of cash, cash equivalents and marketable securities at Comerica at least equivalent to the entire outstanding debt balance with Comerica, which is currently $14.6 million. We must also maintain a monthly liquidity ratio if we draw down on the revolving line of credit.

Fair Value Measurements

We follow accounting guidance on fair value measurements for financial instruments measured on a recurring basis, as well as for certain assets and liabilities that are initially recorded at their estimated fair values. Fair value is defined as the exit price, or the amount that would be received from selling an asset or paid to transfer a liability in an orderly transaction between market participants at the measurement date. We use the following three-level hierarchy that maximizes the use of observable inputs and minimizes the use of unobservable inputs to value our financial instruments:

•

Level 1: Observable inputs such as unadjusted quoted prices in active markets for identical instruments.

•

Level 2: Quoted prices for similar instruments that are directly or indirectly observable in the marketplace.

•

Level 3: Significant unobservable inputs which are supported by little or no market activity and that are financial instruments whose values are determined using pricing models, discounted cash flow methodologies, or similar techniques, as well as instruments for which the determination of fair value requires significant judgment or estimation.

Financial instruments measured at fair value are classified in their entirety based on the lowest level of input that is significant to the fair value measurement. Our assessment of the significance of a particular input to the fair value measurement in its entirety requires us to make judgments and consider factors specific to the asset or liability. The use of different assumptions and/or estimation methodologies may have a material effect on estimated fair values. Accordingly, the fair value estimates disclosed or initial amounts recorded may not be indicative of the amount that we or holders of the instruments could realized in a current market exchange.

The carrying amounts of cash equivalents and marketable securities approximate their fair value based upon quoted market prices. Certain of our financial instruments are not measured at fair value on a recurring basis, but are recorded at amounts that approximate their fair value due to their liquid or short-term nature, such as cash, accounts receivable and payable, and other financial instruments in current assets or current liabilities.

Cash and Cash Equivalents and Concentration of Credit Risk

Cash and cash equivalents consist of cash and short-term, highly-liquid financial instruments that are readily convertible to cash and have maturities of 90 days or less from the date of purchase. They may consist of money market funds, commercial paper, U.S. government agency obligations and corporate notes and bonds with high credit quality. We currently maintain all cash in several institutions in the U.S. Balances at these institutions may exceed Federal Deposit Insurance Corporation insured limits.

Marketable Securities

We have designated our marketable securities as of each balance sheet date as available-for-sale securities and account for them at their respective fair values. Marketable securities are classified as short-term or long-term based on the nature of the securities and their availability to meet current operating requirements. Marketable securities that are readily available for use in current operations are classified as short-term available-for-sale securities and are reported as a component of current assets in the accompanying balance sheets. Marketable securities that are not considered available for use in current operations are classified as long-term available-for-sale securities and are reported as a component of long-term assets in the accompanying balance sheets.

Securities that are classified as available-for-sale are carried at fair value, including accrued interest, with temporary unrealized gains and losses reported as a component of stockholders' deficit until their disposition. We review all available-for-sale securities at each period end to determine if they remain available-for-sale based on our then current intent and ability to sell the security if it is required to do so. The cost of securities sold is based on the specific identification method.

All of our marketable securities are subject to a periodic impairment review. We recognize an impairment charge when a decline in the fair value of our investments below the cost basis is judged to be other-than-temporary.

Property and Equipment

Property and equipment are stated at historical cost less accumulated depreciation and amortization. Additions and improvements are capitalized. Certain costs to internally develop software are also capitalized. Maintenance and repairs are expensed as incurred.

Depreciation and amortization are computed on the straight-line method based on the following estimated useful lives:

Furniture and fixtures

7 years

Equipment

5 years

Computer hardware and software

3 years

We depreciate leasehold improvements associated with operating leases over the shorter of the expected useful life of the improvements or the remaining lease term.

The carrying value for property and equipment is reviewed for impairment at least annually and when events or changes in circumstances indicate that the carrying value of the assets may not be recoverable. In addition, we continue to evaluate our facility needs and may decide to vacate or abandon a portion of one or more of our locations. If we do so, or conclude that we will vacate or abandon space within a defined period, we may recognize impairment charges relating to the remaining book value of any improvements and record as an additional expense the present value of future rent payments, less applicable deferred rent amounts, to the extent it exceeds potential sublet income.

Equity Investments

From time to time, we may enter into collaboration and license agreements under which we receive an equity interest as consideration for all or a portion of up-front, license or other fees under the terms of the agreement. We report equity securities received from non-publicly traded companies in which we do not exercise a significant or controlling interest at cost in other long-term assets in the accompanying balance sheets. We monitor our investments for impairment at least annually, and consider events or changes in circumstances we know of that may have a significant adverse effect on the fair value. We make appropriate reductions in the carrying value if it is determined that an impairment has occurred, based primarily on the financial condition and near and long-term prospects of the issuer. We do not report the fair value of our equity investments because it is not practical to do so.

In July 2013, Array entered into a collaboration agreement with Loxo Oncology, Inc. under which we received shares of convertible, non-voting preferred stock as consideration for licensing rights granted to Loxo. We estimated the fair value of these shares to be $4.5 million based on a valuation analysis prepared with the assistance of a third-party valuation firm. The full estimated value of $4.5 million is reflected as a long-term asset in our balance sheet as of June 30, 2014, and was recorded as license revenue in our statement of operations and comprehensive loss during the first quarter of fiscal 2014. Further discussion regarding assumptions and estimates related to the determination of the fair value of the shares and related revenue recognition can be found in Note 4 - Collaboration and License Agreements – Loxo Oncology, Inc, along with information regarding our percentage of ownership interest in Loxo. See Note 13 – Subsequent Event for additional information about our equity investment in Loxo after July 31, 2014, the effective date of Loxo's initial public offering.

In addition, as of both June 30, 2014 and 2013, we held shares of preferred stock of VentiRx Pharmaceuticals, Inc. ("VentiRx") valued at $1.5 million that we received under a February 2007 collaboration and licensing agreement with VentiRx.

Accrued Outsourcing Costs

Substantial portions of our preclinical studies and clinical trials are performed by third-party laboratories, medical centers, contract research organizations and other vendors (collectively "CROs"). These CROs generally bill monthly or quarterly for services performed, or bill based upon milestone achievement. For preclinical studies, we accrue expenses based upon estimated percentage of work completed and the contract milestones remaining. For clinical studies, expenses are accrued based upon the number of patients enrolled and the duration of the study. We monitor patient enrollment, the progress of clinical studies and related activities to the extent possible through internal reviews of data reported to us by the CROs, correspondence with the CROs and clinical site visits. Our estimates depend on the timeliness and accuracy of the data provided by the CROs regarding the status of each program and total program spending. We periodically evaluate the estimates to determine if adjustments are necessary or appropriate based on information we receive.

Convertible Senior Notes

Our 3.00% convertible senior notes due 2020 are accounted for in accordance with Financial Accounting Standards Board ("FASB") Accounting Standards Codification (“ASC”) 470-20, Debt – Debt with Conversion and Other Options. ASC 470-20 requires the issuer of convertible debt that may be settled in shares or cash upon conversion at the issuer's option, such as our notes, to account for the liability (debt) and equity (conversion option) components separately. The value assigned to the debt component is the estimated fair value, as of the issuance date, of a similar debt instrument without the conversion option. The amount of the equity component (and resulting debt discount) is calculated by deducting the fair value of the liability component from the principal amount of the convertible debt instrument. The resulting debt discount is amortized as additional non-cash interest expense over the expected life of the notes utilizing the effective interest method. Although ASC 470 has no impact on our actual past or future cash flows, it requires us to record non-cash interest expense as the debt discount is amortized. For additional information, see Note 5 – Long-term Debt.

Operating Leases

We have negotiated certain landlord/tenant incentives and rent holidays and escalations in the base price of rent payments under our operating leases. For purposes of determining the period over which these amounts are recognized or amortized, the initial term of an operating lease includes the "build-out" period of leases, where no rent payments are typically due under the terms of the lease and includes additional terms pursuant to any options to extend the initial term if it is more likely than not that we will exercise such options. We recognize rent holidays and rent escalations on a straight-line basis over the initial lease term. The landlord/tenant incentives are recorded as an increase to deferred rent in the accompanying balance sheets and are amortized on a straight-line basis over the initial lease term. We have also entered into two sale-leaseback transactions for our facilities in Boulder and Longmont, Colorado, where the consideration received from the landlord was recorded as an increase to deferred rent in the accompanying balance sheets and is amortized on a straight-line basis over the lease term. Deferred rent balances are classified as short-term or long-term in the accompanying balance sheets based upon the period when reversal of the liability is expected to occur.

Share-Based Compensation

Share-based compensation awards include stock options granted under our Amended and Restated Stock Option and Incentive Plan and purchases of common stock by our employees at a discount to the market price under our Amended and Restated Employee Stock Purchase Plan ("ESPP"). We use the Black-Scholes option pricing model to determine the grant date fair value of stock options and ESPP awards. The determination of the fair value of share-based awards using an option pricing model is affected by our stock price, as well as assumptions regarding a number of complex and subjective variables. Share-based compensation expense is recognized on a straight-line basis over the requisite service period for each award. Further, compensation expense recognized in our statement of operations and comprehensive loss for stock options is reduced for estimated forfeitures, which are based on historical experience and are revised in subsequent periods if actual forfeitures differ from our estimates.

Revenue Recognition

We recognize revenue for the performance of services or the shipment of products when each of the following four criteria is met: (i) persuasive evidence of an arrangement exists; (ii) products are delivered or as services are rendered; (iii) the sales price is fixed or determinable; and (iv) collectability is reasonably assured.

We follow ASC 605-25, Revenue Recognition – Multiple-Element Arrangements and ASC 808, Collaborative Arrangements, if applicable, to determine the recognition of revenue under our collaborative research, development and commercialization agreements. The terms of these agreements generally contain multiple elements, or deliverables, which may include (i) grants of licenses, or options to obtain licenses, to our intellectual property, (ii) research and development services, (iii) drug product manufacturing, and/or (iv) participation on joint research and/or joint development committees. The payments we may receive under these arrangements typically include one or more of the following: non-refundable, up-front license fees; option exercise fees; funding of research and/or development efforts; amounts due upon the achievement of specified objectives; and/or royalties on future product sales.

ASC 605-25 provides guidance relating to the separability of deliverables included in an arrangement into different units of accounting and the allocation of arrangement consideration to the units of accounting. The evaluation of multiple-element arrangements requires management to make judgments about (i) the identification of deliverables, (ii) whether such deliverables are separable from the other aspects of the contractual relationship, (iii) the estimated selling price of each deliverable, and (iv) the expected period of performance for each deliverable.

To determine the units of accounting under a multiple-element arrangement, management evaluates certain separation criteria, including whether the deliverables have stand-alone value, based on the relevant facts and circumstances for each arrangement. Management then estimates the selling price for each unit of accounting and allocates the arrangement consideration to each unit utilizing the relative selling price method. The allocated consideration for each unit of accounting is recognized over the related obligation period in accordance with the applicable revenue recognition criteria.

If there are deliverables in an arrangement that are not separable from other aspects of the contractual relationship, they are treated as a combined unit of accounting, with the allocated revenue for the combined unit recognized in a manner consistent with the revenue recognition applicable to the final deliverable in the combined unit. Payments received prior to satisfying the relevant revenue recognition criteria are recorded as deferred revenue in the accompanying balance sheets and recognized as revenue when the related revenue recognition criteria are met.

We typically receive non-refundable, up-front payments when licensing our intellectual property, which often occurs in conjunction with a research and development agreement. When management believes that the license to our intellectual property has stand-alone value, we generally recognize revenue attributed to the license upon delivery provided that there are no future performance requirements for use of the license. When management believes that the license to our intellectual property does not have stand-alone value, we typically recognize revenue attributed to the license on a straight-line basis over the contractual or estimated performance period. When the performance period is not specifically identifiable from the agreement, we estimate the performance period based upon provisions contained within the agreement, such as the duration of the research or development term.

Most of our agreements provide for non-refundable milestone payments. We recognize revenue that is contingent upon the achievement of a substantive milestone in its entirety in the period in which the milestone is achieved. A milestone is considered substantive when the consideration payable to us for such milestone (i) is consistent with our performance necessary to achieve the milestone or the increase in value to the collaboration resulting from our performance, (ii) relates solely to our past performance and (iii) is reasonable relative to all of the other deliverables and payments within the arrangement. In making this assessment, we consider all facts and circumstances relevant to the arrangement, including factors such as the scientific, regulatory, commercial and other risks that must be overcome to achieve the milestone, the level of effort and investment required to achieve the milestone and whether any portion of the milestone consideration is related to future performance or deliverables.

For payments payable on achievement of milestones that do not meet all of the conditions to be considered substantive, we recognize a portion of the payment as revenue when the specific milestone is achieved, and the contingency is removed, based on the applicable percentage earned of the estimated research or development effort, or other performance obligations that have elapsed, to the total estimated research and/or development effort attributable to the milestone. In other cases, when a non-substantive milestone payment is attributed to our future research or development obligations, we recognize the revenue on a straight-line basis, or other appropriate method, over the estimated remaining research or development effort. Other contingent event-based payments for which payment is either contingent solely upon the passage of time or the result of our partner's or collaborator's performance are recognized when earned.

We periodically review the estimated performance periods under each of our agreements that provide for non-refundable up-front payments, license fees or milestone payments. We adjust the periods over which revenue should be recognized when appropriate to reflect changes in assumptions relating to the estimated performance periods. We could accelerate revenue recognition in the event of early termination of programs or if our expectations change. Alternatively, we could decelerate revenue recognition if programs are extended or delayed. While such changes to our estimates have no impact on our reported cash flows, the amount of revenue recorded in future periods could be materially impacted.

See Note 4 – Collaboration and License Agreements for further information.

Income Taxes

We account for income taxes using the asset and liability method. We recognize the amount of income taxes payable (refundable) for the year as current income tax provision (benefit) and record a deferred income tax provision (benefit) based on changes in deferred tax assets and liabilities. Deferred tax assets and liabilities are determined based on the difference between the financial statement carrying value and the tax basis of assets and liabilities and, using enacted tax rates in effect, reflect the expected effect these differences would have on future taxable income, if any. Valuation allowances are recorded to reduce the amount of deferred tax assets when management cannot conclude it is more likely than not that some or all of the deferred tax assets will be realized. Such allowances are based upon available objective evidence, the expected reversal of temporary differences and projections of future taxable income.

Segments

We operate in one reportable segment and, accordingly, no segment disclosures have been presented herein. All of our equipment, leasehold improvements and other fixed assets are physically located within the U.S., and all agreements with our partners are denominated in U.S. dollars.

Concentration of Business Risks

Significant Partners

The following significant partners contributed greater than 10% of our total revenue during at least one of the periods set forth below. The revenue from these partners as a percentage of total revenue was as follows:

Year Ended June 30,

2014

2013

2012

Novartis International Pharmaceutical Ltd.

28.6

25.5

16.2

Loxo Oncology, Inc.

23.1

—

AstraZeneca AB

12.1

0.2

—

Celgene

8.9

20.6

6.9

Genentech, Inc.

8.5

40.8

Oncothyreon Inc.

8.2

14.4

—

Amgen Inc.

—

34.2

89.4

87.7

98.1

The loss of one or more of our significant partners could have a material adverse effect on our business, operating results or financial condition. We do not require collateral from our partners, though most pay in advance. Although we are impacted by economic conditions in the biotechnology and pharmaceutical sectors, management does not believe significant credit risk exists as of June 30, 2014.

Geographic Information

The following table details revenue by geographic area based on the country in which our partners are located (in thousands):

Year Ended June 30,

2014

2013

2012

North America

24,757

51,608

70,905

Europe

17,153

17,969

13,987

Asia Pacific

168

243

42,078

69,580

85,135

Accounts Receivable

Novartis and Oncothyreon accounted for 75% and 15%, respectively, of our total accounts receivable balances as of June 30, 2014, compared with 91% of our total accounts receivable balances attributable to Novartis as of June 30, 2013.

Net Loss per Share

Basic net loss per share is computed by dividing net loss for the period by the weighted average number of common shares outstanding during the period. Diluted net loss per share reflects the additional dilution from potential issuances of common stock, such as stock issuable pursuant to the exercise of stock options, as well as from the possible conversion of our convertible senior notes and exercise of outstanding warrants. The treasury stock method is used to calculate the potential dilutive effect of these common stock equivalents. Potentially dilutive shares are excluded from the computation of diluted net loss per share when their effect is anti-dilutive. As a result of our net losses for all periods presented, all potentially dilutive securities were anti-dilutive and have been excluded from the computation of diluted net loss per share.

Comprehensive Loss

Comprehensive loss is comprised of net loss and adjustments to unrealized gains and losses on our investments in available-for-sale marketable securities, net of taxes. We display comprehensive loss and its components in our consolidated statements of operations and comprehensive loss.

Recent Accounting Pronouncements

In May 2014, the FASB issued Accounting Standards Update ("ASU") No. 2014-09, Revenue from Contracts with Customers, which requires an entity to recognize the amount of revenue to which it expects to be entitled for the transfer of promised goods or services to customers. ASU No. 2014-09 will replace most existing revenue recognition guidance in U.S. GAAP when it becomes effective. The new standard is effective for us on July 1, 2017. Early application is not permitted. The standard permits the use of either the retrospective or cumulative effect transition method. We are evaluating the effect that ASU No. 2014-09 will have on our financial statements and related disclosures. We have not yet selected a transition method, nor have we determined the effect of the standard on our ongoing financial reporting.

MARKETABLE_SECURITIES

MARKETABLE SECURITIES	12 Months Ended
	Jun. 30, 2014
Marketable Securities [Abstract]	'
MARKETABLE SECURITIES	'
	MARKETABLE SECURITIES

	Marketable securities consisted of the following as of June 30, 2014 (in thousands):


					Gross		Gross
		Amortized			Unrealized		Unrealized			Fair
		Cost			Gains		Losses			Value
	Short-term available-for-sale securities:
	U.S. treasury securities	$	42,184		$	2	$	(1	)	$	42,185

	Mutual fund securities	222			—		—			222

		42,406			2		(1		)	42,407

	Long-term available-for-sale securities:
	Mutual fund securities	640			—		—			640

		640			—		—			640

	Total	$	43,046		$	2	$	(1	)	$	43,047


	Marketable securities consisted of the following as of June 30, 2013 (in thousands):


					Gross		Gross
		Amortized			Unrealized		Unrealized			Fair
		Cost			Gains		Losses			Value
	Short-term available-for-sale securities:
	U.S. treasury securities	$	47,130		$	—	$	(2	)	$	47,128

	Mutual fund securities	377			—		—			377

		47,507			—		(2		)	47,505

	Long-term available-for-sale securities:
	Mutual fund securities	465			—		—			465

		465			—		—			465

	Total	$	47,972		$	—	$	(2	)	$	47,970


	The majority of the mutual fund securities shown in the above tables are securities held under the Array BioPharma Inc. Deferred Compensation Plan.

	The estimated fair value of our marketable securities was classified into fair value measurement categories as follows (in thousands):


		June 30,
		2014			2013

	Quoted prices in active markets for identical assets (Level 1)	$	43,047		$	47,970

	Quoted prices for similar assets observable in the marketplace (Level 2)	—			—

	Significant unobservable inputs (Level 3)	—			—

	Total	$	43,047		$	47,970


	As of June 30, 2014, the amortized cost and estimated fair value of available-for-sale securities by contractual maturity were as follows (in thousands):


	Amortized			Fair
	Cost			Value

Due in one year or less	$	42,406		$	42,407

Due in one year to three years	640			640

Total	$	43,046		$	43,047

PROPERTY_AND_EQUIPMENT_NET

PROPERTY AND EQUIPMENT, NET	12 Months Ended
	Jun. 30, 2014
Property, Plant and Equipment [Abstract]	'
PROPERTY AND EQUIPMENT, NET	'
	PROPERTY AND EQUIPMENT, NET

	Property and equipment, net consists of the following (in thousands):


		June 30,
		2014			2013

	Furniture and fixtures	$	3,421		$	3,396

	Equipment	40,150			40,183

	Computer hardware and software	14,705			13,552

	Leasehold improvements	32,171			31,406

	Property and equipment, gross	90,447			88,537

	Less: accumulated depreciation and amortization	(82,290		)	(78,488		)
	Property and equipment, net	$	8,157		$	10,049

COLLABORATION_AND_LICENSE_AGRE

COLLABORATION AND LICENSE AGREEMENTS	12 Months Ended
	Jun. 30, 2014
Collaboration and License Agreements [Abstract]	'
COLLABORATION AND LICENSE AGREEMENTS	'
	COLLABORATION AND LICENSE AGREEMENTS

	Celgene

	Array and Celgene Corporation and Celgene Alpine Investment Co., LLC (collectively "Celgene") entered into a Drug Discovery and Development Option and License Agreement in July 2013 to collaborate on development of an Array-invented preclinical development program targeting a novel inflammation pathway. The agreement provides Celgene an option to select multiple clinical development candidates that Celgene may further develop on an exclusive basis under the agreement. Celgene also has the option to obtain exclusive worldwide rights to commercialize one or more of the development compounds it selects upon payment of an option exercise fee to Array. Array will be responsible for funding and conducting preclinical discovery research on compounds directed at the target, and Celgene will be responsible for all clinical development and commercialization of any compounds it selects.

	Array received a non-refundable up-front payment of $11 million from Celgene during the first quarter of fiscal 2014. Array is also eligible to receive potential milestone payments of up to $376 million based upon achievement of development, regulatory and sales objectives identified in the agreement, plus royalties on net sales of all drugs. Additionally, Array will retain all rights to the program if Celgene does not exercise its option.

	Pursuant to the accounting guidance for revenue recognition for multiple-element arrangements, we determined that Array is obligated to deliver three non-contingent deliverables related to the Celgene agreement. These deliverables are (i) the performance of research services under the discovery program (the "research services deliverable"), (ii) a non-exclusive license granted to Celgene to certain Array and collaboration technology for the sole purpose of being able to perform collaboration activities and (iii) participation on the joint research committee ("JRC"). The Celgene agreement provides for no general right of return for any non-contingent deliverable. Both the research services deliverable and the JRC deliverable meet the separation criteria; however, the non-exclusive license deliverable has no value outside of the collaboration, therefore, it does not meet the separation criteria and is recognized as a combined unit of accounting with the research services deliverable. The research services deliverable and the JRC deliverable are both expected to be delivered throughout the duration of the option term, which is the period of time between the effective date of the agreement and the earlier of a specified amount of time after the completion of certain preclinical studies to be conducted under the Celgene agreement, or three years after the effective date. The option term may be extended by Celgene for an additional one-year period under certain circumstances specified in the agreement.

	The exclusive license that Celgene may obtain by exercising its option and paying an exercise fee to Array is a contingent deliverable due to the uncertainty regarding whether Celgene will exercise its option. Therefore, we did not allocate any of the up-front payment received to this contingent deliverable.

	Determining a selling price for the research services deliverable required the use of certain estimates, including our estimate for the expected length of the option term, which we currently believe to be three years, and the number of full-time employees ("FTEs") required for the conduct of the discovery program. We utilized vendor-specific objective evidence for our FTE costs related to activities to be performed by Array scientists, as well as third-party estimates to determine the costs of the preclinical studies that we plan to outsource. We estimated a selling price for the JRC deliverable by estimating the time required for our scientists to perform their obligations and utilized our established FTE rate for research services as an estimate of what we would bill for this time if we sold this deliverable on a stand-alone basis.

	The majority of the up-front payment is for the performance of research services. We recognized $3.7 million of this payment in collaboration revenue during the year ended June 30, 2014, and will recognize the rest of the up-front payment over the remainder of the three-year estimated option term.

	The Celgene agreement will continue on a country-by-country basis until the termination of the royalty payment obligations or, if earlier, the termination of the agreement in accordance with its terms. The agreement may be terminated by either party for an uncured material breach by the other party. In addition, Celgene may terminate the agreement in its entirety or as to any collaboration compound by giving Array six months' prior notice, and in any such event the rights to any terminated programs would revert to Array and Celgene’s obligation to pay milestones or royalties with respect to any terminated programs would terminate. If Celgene does not exercise its option to obtain an exclusive license, the period of exclusivity to be observed by Array under the agreement will end upon expiration of the option term. If Celgene does exercise its option, the period of exclusivity will continue as long as Celgene either has an active development program for, or is commercializing, a compound selected under the agreement, and Array continues to be entitled to receive milestones or royalties under the agreement. Array and Celgene have also agreed to indemnify the other party for breaches of their respective representations and warranties under the agreement and certain of their respective activities under the agreement.

	Genentech, Inc.

	We entered into a Licensing and Collaboration Agreement with Genentech in December 2003 for development of small molecule drugs invented by Array directed at multiple therapeutic targets in the field of oncology. In August 2011, we entered into a License Agreement with Genentech for the development of each company’s small-molecule Checkpoint kinase 1 ("Chk-1") program in oncology.

	Under the 2003 agreement, Genentech made an up-front payment and provided research funding to Array, and we are entitled to receive additional milestone payments based on achievement of certain development and commercialization milestones and royalties on certain resulting product sales under the agreement. The 2003 agreement was expanded in 2005, 2008, and 2009 to develop clinical candidates directed against additional targets and, in 2010, the term of funded research was extended through January 2013, after which the research term ended. We have received up-front and milestone payments totaling $23.5 million under the 2003 agreement. We are eligible to earn an additional $24.0 million in payments if Genentech continues development and achieves the remaining milestones set forth in the 2003 agreement.

	The partnered drugs under the Chk-1 agreement include Genentech’s compound GDC-0425 and Array’s compound GDC-0575 (ARRY-575). In 2014, Genentech selected GDC-0575 over GDC-0425 to advance into further clinical trials. Under the terms of the Chk-1 collaboration agreement, Genentech acquired a license to Array’s compound GDC-0575 and is responsible for all clinical development and commercialization activities. We received an up-front payment of $28.0 million during the first quarter of fiscal 2012 and are eligible to receive payments of up to $380 million based on the achievement of clinical and commercial milestones under this agreement. We will also receive up to double-digit royalties on sales of any drugs resulting from the Chk-1 agreement.

	Pursuant to the accounting guidance for revenue recognition for multiple-element arrangements, we determined that Array is obligated to deliver three non-contingent deliverables related to the Chk-1 agreement that meet the separation criteria and therefore are treated as separate units of accounting. These deliverables are (i) the delivery of specified clinical materials for GDC-0575 for use in future clinical trials, (ii) the transfer of the license and related technology with ongoing regulatory services to assist in filing the Investigational New Drug ("IND") application and to provide supporting data, and (iii) activities related to the achievement of a specified milestone. The Chk-1 agreement provides for no general right of return for any non-contingent deliverable.

	The first non-contingent deliverable required Array to prepare specified clinical materials for delivery to Genentech. We completed this delivery in December 2011. The second obligation, related to the non-contingent deliverable to assist in filing the IND application, was completed as of March 31, 2012. Revenue for both of these deliverables has been recognized in full. We are recognizing revenue allocated to the third obligation over the period from inception of the Chk-1 agreement until such time that the specified milestone is achieved.

	The Chk-1 agreement also includes a contingent deliverable whereby Genentech could, at its sole option, require us to perform chemical and manufacturing control ("CMC") activities for additional drug product or improved processes. The CMC option is a contingent deliverable because the scope, likelihood and timing of the potential services are unclear. Certain critical terms of the services have not yet been negotiated, including the fee that we would receive for the service and Genentech could elect to acquire the drug materials without our assistance either by manufacturing them in-house or utilizing a third-party vendor. Therefore, no portion of the up-front payment has been allocated to the contingent CMC services that we may be obligated to perform in the future.

	The determination of the stand-alone value for each non-contingent deliverable under the Chk-1 agreement required the use of significant estimates, including estimates of the time to complete the transfer of related technology and to assist in filing the IND. Further, to determine the stand-alone value of the license and initial milestone, we considered the negotiation discussions that led to the final terms of the agreement, publicly-available data for similar licensing arrangements between other companies and the economic terms of previous collaborations Array has entered into with other partners. We also considered the likelihood of achieving the initial milestone based on our historical experience with early stage development programs and on the ability to achieve the milestone with either of the two partnered drugs, GDC-0425 or GDC-0575. Taking into account these factors, we allocated a portion of the up-front payment to the first milestone. No portion of any revenue recognized is refundable.

	We recognized license and milestone revenue under both agreements of $3.4 million, $5.3 million and $25.9 million during the years ended June 30, 2014, 2013 and 2012, respectively. We also recognized $2.3 million and $8.8 million in collaboration revenue under the 2003 agreement during the years ended June 30, 2013 and 2012, respectively. We recognized $135 thousand in collaboration revenue during the current fiscal year for reimbursable patent expenses.

	Genentech may terminate the 2003 agreement in its entirety upon four months' written notice to Array, and may terminate the Chk-1 agreement upon 60 days' written notice to Array. Under the Chk-1 agreement, either party may terminate upon a material breach by the other party that is not cured within the specified time period. If Genentech terminates the Chk-1 agreement due to a material breach by Array, the license granted to Genentech becomes irrevocable and the royalty to Array will be reduced to a specified percentage. If the Chk-1 agreement is terminated by Genentech for convenience or by Array due to a material breach by Genentech, the license granted to Genentech will terminate, Genentech will continue to be required to pay milestone and royalty payments on any programs for which Genentech had initiated clinical development and Array's exclusivity obligations will continue so long as Genentech is developing or commercializing at least one product subject to the Chk-1 agreement. Array and Genentech have also agreed to indemnify the other party for breaches of representations or warranties made under the Chk-1 agreement and for certain of their respective activities under the Chk-1 agreement.

	Loxo Oncology, Inc.

	In July 2013, Array entered into a Drug Discovery Collaboration Agreement with Loxo and granted Loxo exclusive rights to develop and commercialize certain Array-invented compounds targeted at the tropomyosin kinase ("Trk") family of receptors, including LOXO-101, which is currently in a Phase 1 clinical trial. In April 2014, Array and Loxo amended the agreement and, as a result, the research activities under the agreement were expanded. Under the terms of the amended agreement, Loxo will fund further preclinical research to be conducted by Array during the remainder of the three-year discovery research phase, which may be extended by Loxo for up to two additional one-year renewal periods. In addition, Loxo will fund further discovery and preclinical research to be conducted by Array directed at other targets during the research phase of the agreement. Loxo will be responsible for all additional preclinical and clinical development and commercialization.

	In consideration of the exclusive license and rights granted to Loxo under the agreement, Array received shares of Loxo convertible, non-voting preferred stock representing an initial 19.9% interest in the newly-formed entity; following additional financings by Loxo, Array's ownership interest in Loxo as of June 30, 2014 was 15.3%. All of the shares of preferred stock held by Array converted automatically into shares of common stock on July 31, 2014, the effective date of Loxo's initial public offering, and now represent an approximately 10% ownership interest in Loxo. Array also receives advance payments for preclinical research and other services that Array is providing during the term of the discovery program and is eligible to receive up to $435 million in milestone payments if certain clinical, regulatory and sales milestones are achieved plus royalties on sales of any resulting drugs.

	Pursuant to the accounting guidance for revenue recognition for multiple-element arrangements, we determined that Array is obligated to deliver three non-contingent deliverables related to the amended Loxo agreement. These deliverables are (i) the conduct of the research activities under the discovery program, including related technology transfer (the "research services deliverable"), (ii) an exclusive worldwide license granted to Loxo to certain Array technology and Array's interest in collaboration technology, as well as exclusive worldwide marketing rights (the "license deliverable") and (iii) participation on the JRC. The Loxo agreement provides for no general right of return for any non-contingent deliverable. All of the identified non-contingent deliverables meet the separation criteria; therefore, they are each treated as separate units of accounting. Delivery of the research services and JRC participation obligations will be completed throughout the remainder of the three-year discovery program term. The license deliverable was complete as of September 30, 2013.

	To determine the stand-alone value of the license, we considered our negotiation discussions with Loxo that led to the final terms of the agreement, publicly-available data for similar licensing arrangements between other companies and the economic terms of previous collaborations Array has entered into with other partners. We also considered the estimated valuation of the Series A-1 shares performed by an independent third-party and concluded that this value reasonably approximated the estimated selling price of the related license. We determined a selling price for the research services deliverable using our established annual FTE rate, which represents vendor-specific objective evidence for any FTE costs related to activities to be performed by Array scientists. We determined an estimated selling price for the JRC deliverable by estimating the time required for our scientists to perform their obligations and utilized our established FTE rate for research services as an estimate of what we would bill for this time if we sold this deliverable on a stand-alone basis.

	The receipt of the preferred shares was in consideration for the license deliverable. We allocated an amount of consideration under the Loxo agreement to the license deliverable equal to the fair value of the shares received after consideration of the other factors above. We chose the fair value of the shares received as this was a more evident and readily determinable measure as compared to the alternative method for determining the consideration to allocate to the license deliverable, which was the fair value for the exclusive license. The valuation of the preferred shares required the use of significant assumptions and estimates, including assumptions about the estimated volatility of the equity, the estimated time to a liquidity event, and the likelihood of Loxo obtaining additional future financing.

	The remaining consideration under the amended Loxo agreement, which Loxo pays to Array in advance quarterly payments, was allocated between the research services and JRC participation deliverables and will be recognized as the services are rendered throughout the discovery program term.

	The April 2014 amendment added several contingent deliverables related to either increasing the number of FTEs performing research services for Loxo on a monthly basis in exchange for an advance payment, or rights to discontinue research activities for fewer targets in exchange for additional payments to be made to Array. All of the obligations added to the arrangement by the amendment were considered contingent because the likelihood and timing of these deliverables is uncertain and therefore, the potential consideration associated with these obligations was not included in the total allocable consideration.
	We recognized the full $4.5 million estimated fair value of the preferred shares received in license revenue during the first quarter of fiscal 2014, as delivery of the shares was not contingent upon either the delivery of additional items or meeting other specified performance conditions. We also recognized $5.2 million in collaboration revenue during the year ended June 30, 2014.

	The amended Loxo agreement will continue on a country-by-country basis until the termination of the royalty payment obligations, unless terminated earlier by the parties in accordance with its terms. The agreement may be terminated by either party upon the failure of the other party to cure any material breach of its obligations under the agreement, provided that, so long as Loxo is reasonably able to pay its debts as they are due, Array will only be entitled to seek monetary damages, and will not have the right to terminate the amended agreement in the event of Loxo's breach after expiration of the discovery program term. Loxo also has the right to terminate the amended agreement or to terminate discovery research with respect to any targets under development with six months' notice to Array. If Loxo terminates the amended agreement for convenience, all licenses granted to Loxo will terminate and Array will have all rights to further develop and commercialize the licensed programs. The period of exclusivity to be observed by Array under the amended Loxo agreement will continue as long as Loxo either has an active research and/or development program for a target and the program could result in the receipt of milestones or royalties under the program by Array, or as long as Loxo is commercializing a product for a target under the amended agreement.

	Novartis International Pharmaceutical Ltd.

	Array entered into a License Agreement with Novartis in April 2010, which grants Novartis the exclusive worldwide right to develop and commercialize binimetinib, as well as other specified MEK inhibitors. Under the Novartis agreement, we have elected to conduct further development of binimetinib as a single agent in a Phase 3 trial of patients with low-grade serous ovarian cancer. Novartis is responsible for all other development activities and for the commercialization of products under the agreement, subject to our option to co-detail approved drugs in the U.S.

	In consideration for the rights granted to Novartis under the agreement, we received $45 million in the fourth quarter of fiscal 2010, which was comprised of an up-front fee and a milestone payment. In March 2011, we earned a $10 million milestone payment which was received in the fourth quarter of fiscal 2011. In June 2013, we earned a $5 million milestone payment, which was received during the first quarter of fiscal 2014. We are eligible to receive up to approximately $408 million in additional aggregate milestone payments if all clinical, regulatory and commercial milestones specified in the Novartis agreement are achieved for binimetinib. Novartis will also pay us royalties on worldwide sales of any approved drugs. In addition, as long as we continue to co-develop products under the program, the royalty rate on U.S. sales is significantly higher than the rate on sales outside the U.S., as described below under Co-Development Arrangement.

We recognized the up-front fee and milestone payments on a straight-line basis from April 2010 through April 2014. During the years ended June 30, 2014, 2013 and 2012, we recognized $8.0 million, $10.0 million and $10.0 million, respectively, of license revenue and $4.0 million, $7.7 million and $3.8 million, respectively, of milestone revenue under the Novartis agreement.

The Novartis agreement will be in effect on a product-by-product and country-by-country basis until no further payments are due with respect to the applicable product in the applicable country, unless terminated earlier. Either party may terminate the agreement in the event of an uncured material breach of a material obligation under the agreement by the other party upon 90 days' prior notice. Novartis may terminate portions of the agreement following a change in control of Array and may terminate the agreement in its entirety or on a product-by-product basis with 180 days' prior notice. Array and Novartis have each further agreed to indemnify the other party for manufacturing or commercialization activities conducted by it under the agreement, or for negligence, willful misconduct or breach of covenants, warranties or representations made by it under the agreement.

Co-Development Arrangement

The Novartis agreement also contains co-development rights whereby we can elect to pay a share of the combined total development costs, subject to a maximum amount with annual caps. During the first two years of the co-development period, Novartis reimbursed us for 100% of our development costs. We began to pay our share of the combined development costs that had accrued since inception of the program, with payments to Novartis of $9.2 million and $11.3 million in the second quarters of fiscal 2013 and fiscal 2014, respectively, in accordance with the terms of the Novartis agreement. During fiscal 2014, we committed to continue our co-development contribution through fiscal 2015. We have the right to opt out of paying our share of the combined development costs on an annual basis after fiscal 2015, in which case, the U.S. royalty rate would then be reduced for any such product based on a pre-specified formula, subject to a minimum that equals the royalty rate on sales outside the U.S. Additionally, we would no longer have the right to develop or co-detail such product.

We record a receivable in accounts receivables on the balance sheet for the amounts due from Novartis for the reimbursement of our development costs in excess of the annual cap. We record expense in cost of partnered programs on the statement of operations and comprehensive loss for our share of the combined development costs and accrue these costs on our balance sheet in co-development liability.

Our share of the combined development costs was $18.9 million, $11.8 million and $5.6 million during the years ended June 30, 2014, 2013 and 2012, respectively. We recorded co-development liabilities of $16.2 million and $11.0 million as of June 30, 2014 and 2013, respectively. We had related receivables of $4.1 million and $3.7 million as of June 30, 2014 and 2013, respectively, for the reimbursable development costs we incurred during the respective preceding three-month periods in excess of the annual cap.

Oncothyreon Inc.

In May 2013, we entered into a Development and Commercialization Agreement with Oncothyreon to collaborate on the development and commercialization of ARRY-380, now also known as ONT-380, for the treatment of cancer. Under the terms of the agreement, Oncothyreon paid Array a one-time up-front fee of $10 million and received a license to ARRY-380 enabling it to perform its development activities. Oncothyreon will be responsible for conducting the clinical development of ARRY-380 through a defined set of proof-of-concept trials and will also be responsible for all development costs incurred by or on behalf of either party with respect to these proof-of-concept trials.

Unless Array opts out of further development and commercialization, as described below, Array will reimburse Oncothyreon for the proof-of-concept development costs through a mechanism whereby Array bears a disproportionate amount of Phase 3 development costs and Oncothyreon receives a disproportionate amount of the profits in the U.S. until Oncothyreon is repaid a percentage of the amounts it has spent on the proof-of-concept trials. Oncothyreon and Array will jointly conduct any Phase 3 development supported by the proof-of-concept studies. Subject to certain exceptions primarily related to the reimbursement provisions described above, Oncothyreon and Array will each be responsible for 50% of the development costs incurred with respect to any Phase 3 development.

Array is responsible for worldwide commercialization of the product. Oncothyreon has a 50% co-promotion right in the U.S. Each party also retains the right to opt out of further development and commercialization in exchange for a royalty. Subject to certain exceptions, Oncothyreon and Array will bear, or be entitled to, 50% of the profit or loss from commercializing the product in the U.S. Outside of the U.S., Oncothyreon will receive a double-digit royalty on net sales intended to approximate a 50% profit share, and the two companies will share equally the proceeds from any sublicense of marketing rights.

Following the proof-of-concept trials, both Array and Oncothyreon are currently expected to be active participants in the collaboration and will jointly (50/50) share risks and rewards under the agreement. Accordingly, the collaborative activities not included in the proof-of-concept studies under the Oncothyreon agreement should be accounted for under ASC 808, Collaborative Arrangements and, as such, these collaborative activities were separated from the deliverables under the Oncothyreon agreement. Additionally, the up-front consideration is not related to any performance of the collaborative activities and is not refundable; therefore, none of the up-front payment was attributed to the collaborative activities.

Pursuant to the accounting guidance for revenue recognition for multiple-element arrangements, we determined that in order for Oncothyreon to be able to conduct its activities during the proof-of-concept trials, Array is obligated to deliver three non-contingent deliverables related to the Oncothyreon agreement that meet the separation criteria and therefore are treated as separate units of accounting. These deliverables are (i) the license deliverable, which includes the initial technology transfer, as well as the transfer of regulatory information necessary for Oncothyreon to file its own IND, (ii) the transfer of existing quantities of clinical product, and (iii) participation on the joint development committee ("JDC") during the proof-of concept activities. The Oncothyreon agreement provides for no general right of return for any non-contingent deliverable. The first non-contingent deliverable for the license deliverable was completed as of June 30, 2013. The second non-contingent deliverable requiring Array to deliver existing quantities of clinical materials of ARRY-380 is expected to be completed by the end of the first quarter of fiscal 2015, and the final obligation requiring us to participate on the JDC will be completed over the estimated time frame of the proof-of-concept activities.

The Oncothyreon agreement also includes contingent deliverables for the future manufacture and supply of additional drug product for the studies and for the rendering of support and advisory services by Array to Oncothyreon during the proof-of-concept trials. These deliverables are considered contingent because the scope, likelihood and timing of the potential services are unclear. We could elect to manufacture the additional drug materials in-house or by utilizing a third-party vendor. Additionally, we are not required to have any individuals devoted to supporting Oncothyreon, and we will charge our costs to the development program as they are incurred. Therefore, no portion of the up-front payment has been allocated to the contingent deliverables that we may be obligated to perform in the future.

To determine the stand-alone value of the license deliverable, we considered the differences between this agreement and the licensing agreements with our other partners, publicly-available data for similar licensing arrangements between other companies and the economic terms of previous collaborations Array has entered into with other partners. We also considered clinical trial success rates in the industry. Taking into account these factors, as well as the stand-alone values for the delivery of existing drug product and JDC participation, all of the up-front payment was allocated to the license deliverable. No portion of any revenue recognized is refundable.

We recognized $3.5 million in collaboration revenue, including $2.6 million for reimbursable expenses, during the year ended June 30, 2014. Additionally, we recognized $10.0 million in license and milestone revenue during the year ended June 30, 2013, related to the up-front payment.

The Oncothyreon agreement will continue on a country-by-country basis until the termination of the royalty payment obligations, or if earlier, the termination of the agreement in accordance with its terms. The Oncothyreon agreement may be terminated by Array upon Oncothyreon's uncured failure to timely initiate committed trials or complete certain development activities, and may also be terminated under certain other circumstances, including material breach, as set forth in the agreement. Array and Oncothyreon have also agreed to indemnify the other party for certain of their respective activities under the agreement.

Deferred Revenue

Deferred revenue consisted of the following (in thousands):


	June 30,
	2014			2013

Celgene	$	7,258		$	—

Biogen Idec	1,218			—

Loxo Oncology, Inc.	625			—

Genentech, Inc.	367			2,300

Novartis International Pharmaceutical Ltd.	—			12,053

Other partners	78			—

Total deferred revenue	9,546			14,353

Less: Current portion	(6,193		)	(14,353		)
Deferred revenue, long-term portion	$	3,353		$	—

LONGTERM_DEBT

LONG-TERM DEBT	12 Months Ended
	Jun. 30, 2014
Debt Disclosure [Abstract]	'
LONG-TERM DEBT	'
	LONG-TERM DEBT

	Long-term debt consists of the following (in thousands):


		June 30,
		2014				2013

	Comerica term loan	$	14,550			$	14,550

	Convertible senior notes	132,250				132,250

	Long-term debt, gross	146,800				146,800

	Less: Unamortized debt discount	(42,848		)		(47,779		)
	Long-term debt, net	$	103,952			$	99,021


	Comerica Bank

	We entered into a Loan and Security Agreement with Comerica Bank dated June 28, 2005, which has been subsequently amended and provides for a $15 million term loan and a revolving line of credit of $6.8 million. The term loan bears interest at a variable rate and we currently have $14.6 million outstanding under the term loan. The revolving line of credit was established to support standby letters of credit in relation to our facilities leases, and has not been drawn upon.

	Effective December 31, 2013, the Loan and Security Agreement was amended to extend the maturity date of the term loan to October 2017 and to extend the maturity date of the revolving line of credit to June 2015. Also effective December 31, 2013, the interest rate on the term loan was amended to be equal to the Prime Rate, if the balance of our cash, cash equivalents and marketable securities maintained at Comerica is greater than or equal to $10 million, or equal to the Prime Rate plus 2% if this balance is less than $10 million. As of June 30, 2014, the term loan with Comerica had an interest rate of 3.25% per annum.

	The amendment to the Loan and Security Agreement also modified covenants requiring certain minimum monthly ending balances of total cash, cash equivalents and marketable securities to be maintained at Comerica based on our overall outstanding cash, cash equivalents and marketable securities. Effective December 31, 2013, this prior covenant was replaced with a covenant that requires us to maintain a balance of cash at Comerica that is at least equivalent to our total outstanding obligation under the term loan if our overall balance of cash, cash equivalents and marketable securities at Comerica and approved outside accounts is less than $22 million.

	The amendment further added a financial covenant that applies if we draw down on the revolving line of credit. In this event, we must maintain a ratio equal to at least 1.25 to 1.00 as of the last day of each month commencing December 31, 2013, and calculated as follows: (A) total cash, cash equivalents and marketable securities less all outstanding obligations to Comerica under the term loan, plus specified percentages of the respective values of eligible accounts, equipment and eligible inventory, divided by (B) the aggregate amount outstanding under the revolving letter of credit sublimit. No amounts are outstanding under the revolving line of credit and we do not expect to make any draws under this facility.

	Our obligations under the Loan and Security Agreement are secured by a first priority security interest in all of our assets, other than our intellectual property. The Loan and Security Agreement contains representations and warranties and affirmative and negative covenants that are customary for credit agreements of this type. Our ability to, among other things, sell certain assets, engage in a merger or change in control transaction, incur debt, pay cash dividends and make investments, are restricted by the Loan and Security Agreement. The Loan and Security Agreement also contains events of default that are customary for credit agreements of this type, including payment defaults, covenant defaults, insolvency type defaults and events of default relating to liens, judgments, material misrepresentations and the occurrence of certain material adverse events.

	We use a discounted cash flow model to estimate the fair value of the Comerica term loan. The fair value was estimated at $14.6 million as of both June 30, 2014 and 2013, and was classified using Level 2, observable inputs other than quoted prices in active markets.

	3.00% Convertible Senior Notes Due 2020

	On June 10, 2013, through a registered underwritten public offering, we issued and sold $132.3 million aggregate principal amount of 3.00% convertible senior notes due 2020 (the "Notes"), resulting in net proceeds to Array of approximately $128.0 million after deducting the underwriting discount and estimated offering expenses.

	The Notes are the general senior unsecured obligations of Array. The Notes bear interest at a rate of 3.00% per year, payable semi-annually on June 1 and December 1 of each year, commencing December 1, 2013. The Notes will mature on June 1, 2020, unless earlier converted by the holders or redeemed by us.

	Prior to March 1, 2020, holders may convert the Notes only upon the occurrence of certain events described in a supplemental indenture we entered into with Wells Fargo Bank, N.A., as trustee, upon issuance of the Notes. On or after March 1, 2020, until the close of business on the scheduled trading day immediately prior to the maturity date, holders may convert their Notes at any time. Upon conversion, the holders will receive, at our option, shares of our common stock, cash or a combination of shares and cash. The Notes will be convertible at an initial conversion rate of 141.8641 shares per $1,000 in principal amount of Notes, equivalent to a conversion price of approximately $7.05 per share. The conversion rate is subject to adjustment upon the occurrence of certain events described in the supplemental indenture. Holders of the Notes may require us to repurchase all or a portion of their Notes for cash at a price equal to 100% of the principal amount of the Notes to be purchased, plus accrued and unpaid interest, if there is a qualifying change in control or termination of trading of our common stock.

	On or after June 4, 2017, we may redeem for cash all or part of the outstanding Notes if the last reported sale price of our common stock exceeds 130% of the applicable conversion price for 20 or more trading days in a period of 30 consecutive trading days ending within seven trading days immediately prior to the date we provide the notice of redemption to holders. The redemption price will equal 100% of the principal amount of the Notes to be redeemed, plus all accrued and unpaid interest. If we were to provide a notice of redemption, the holders could convert their Notes up until the business day immediately preceding the redemption date.

	In accordance with ASC Subtopic 470-20, we used an effective interest rate of 10.25% to determine the liability component of the Notes. This resulted in the recognition of $84.2 million as the liability component of the Notes and the recognition of the residual $48.0 million as the debt discount with a corresponding increase to additional paid-in capital for the equity component of the Notes. The underwriting discount and estimated offering expenses of $4.3 million were allocated between the debt and equity issuance costs in proportion to the allocation of the liability and equity components of the Notes. Debt issuance costs of $2.7 million were included in other long-term assets on our balance sheet as of the issuance date. Equity issuance costs of $1.6 million were recorded as an offset to additional paid-in capital. The debt discount and debt issuance costs will be amortized as non-cash interest expense through June 1, 2020. The balance of unamortized debt issuance costs was $2.4 million as of June 30, 2014.

	The fair value of the Notes was $132.3 million and $126.0 million at June 30, 2014 and 2013, respectively, and was determined using Level 2 inputs based on their quoted market values.

	Deerfield Credit Facilities

	We had two outstanding credit facilities with Deerfield, which we repaid in full on June 10, 2013, with $92.6 million of the net proceeds from the issuance of the Notes. Under the terms of our credit facilities with Deerfield, we issued warrants to Deerfield that remain outstanding and which are discussed further in Note 7 - Stockholders' Deficit. At the time of their issuance, we recorded the value of the warrants as debt discount. The Deerfield credit facilities also had two features relating to variable interest and a put option that were characterized as embedded derivatives and whose initial value was also recorded as debt discount.

	At the time of prior repayments and the final repayment of principal under the Deerfield credit facilities, we adjusted the debt discount and outstanding transaction fees recognized by the same proportion as the percentage of debt that was repaid and recognized a corresponding loss on prepayment of long-term debt, net in our statements of operations and comprehensive loss. Ultimately, the remaining outstanding balances of debt discount and debt transaction fees were written off upon repayment of the credit facilities as follows (in thousands):


		Year Ended June 30,
		2013				2012

	Write off proportional value or remaining balance of the debt discount	$	(10,898	)		$	(887	)
	Write off proportional value or remaining balance of the unamortized debt issuance costs	(720		)		(55		)

	Fair value adjustment for, or write off of, the embedded derivatives	421				—

	Loss on prepayment of long-term debt, net	$	(11,197	)		$	(942	)

Summary of Interest Expense

The following table shows the details of our interest expense for all of our debt arrangements outstanding during the periods presented, including contractual interest, and amortization of debt discount, debt issuance costs and loan transaction fees that were charged to interest expense (in thousands):


	Year Ended June 30,
	2014				2013				2012
Comerica Term Loan
Simple interest	$	479			$	483			$	489

Amortization of fees paid for letters of credit	48				107				108

Total interest expense on the Comerica term loan	527				590				597


Convertible Senior Notes
Contractual interest	3,979				221				—

Amortization of debt discount	4,932				259				—

Amortization of debt issuance costs	278				14				—

Total interest expense on the convertible senior notes	9,189				494				—


Deerfield Credit Facilities
Simple interest	—				6,078				6,492

Amortization of debt discounts and transaction fees	—				4,331				4,419

Change in fair value of the embedded derivatives	—				(235		)		116

Total interest expense on the Deerfield credit facilities	—				10,174				11,027

Total interest expense	$	9,716			$	11,258			$	11,624


Commitment Schedule

We are required to make principal payments for our long-term debt as follows during the fiscal years ending June 30 (in thousands):


	Principal Due

2015	$	—

2016	—

2017	—

2018	14,550

2019	—

Thereafter	132,250

	$	146,800

COMMITMENTS_AND_CONTINGENCIES

COMMITMENTS AND CONTINGENCIES	12 Months Ended
	Jun. 30, 2014
Commitments and Contingencies Disclosure [Abstract]	'
COMMITMENTS AND CONTINGENCIES	'
	COMMITMENTS AND CONTINGENCIES

	Operating Leases

	We lease facilities and equipment under various non-cancelable operating leases that expire through 2016. Most of our leases for facilities include an option to extend the lease for up to two terms of five years each. In addition to minimum lease payments, we are contractually obligated under some of our lease agreements to pay certain operating expenses during the term of the lease, such as maintenance, taxes and insurance.

	Future minimum rental commitments for our operating leases, by fiscal year and in the aggregate, as of June 30, 2014, are (in thousands):


			Rental Payments

	2015		$	8,316

	2016		8,338

	2017		368

	2018		—

	2019		—

	Thereafter		—

			$	17,022


	Rent expense under these agreements follows (dollars in thousands):


		Year Ended June 30,
		2014			2013			2012

	Cash paid for rent	$	8,878		$	8,625		$	8,549

	Deferred rent credits	(3,645		)	(3,489		)	(3,332		)
	Rent expense, net	$	5,233		$	5,136		$	5,217


	Legal Proceedings

	From time to time, we may be involved in claims or lawsuits that arise in the ordinary course of business. Accruals for claims or lawsuits are provided to the extent that losses are deemed both probable and estimable. Although the ultimate outcome of these claims or lawsuits cannot be ascertained, on the basis of present information and advice received from counsel, it is management's opinion that the disposition or ultimate determination of such claims or lawsuits will not have a material adverse effect on Array.

STOCKHOLDERS_DEFICIT

STOCKHOLDERS' DEFICIT	12 Months Ended
	Jun. 30, 2014
Equity [Abstract]	'
STOCKHOLDERS' DEFICIT	'
	STOCKHOLDERS’ DEFICIT

	Stock Option and Incentive Plan

	In September 2000, our Board of Directors approved the Amended and Restated Stock Option and Incentive Plan (the "Option and Incentive Plan"). As of June 30, 2014, 23,131,696 shares of common stock are reserved for future issuance under the Option and Incentive Plan to our eligible employees, consultants and directors. Of the shares available for future issuance, 1,690,965 are available for issuance as incentive stock options. The remaining shares can be used for other awards. In addition, the Option and Incentive Plan provides for the reservation of additional authorized shares on any given day in an amount equal to the difference between:

	(i)	25% of our issued and outstanding shares of common stock, on a fully diluted and as-converted basis; and

	(ii)	the number of outstanding shares relating to awards under the Option and Incentive Plan plus the number of shares available for future grants of awards under the Option and Incentive Plan on that date.

	However, in no event shall the number of additional authorized shares determined pursuant to this formula exceed, when added to the number of shares of common stock outstanding and reserved for issuance under the Option and Incentive Plan other than pursuant to this formula, under the ESPP and upon conversion or exercise of outstanding warrants or convertible securities, the total number of shares of common stock authorized for issuance under our Amended and Restated Certificate of Incorporation.

	The Option and Incentive Plan provides for awards of both non-statutory stock options and incentive stock options within the meaning of Section 422 of the Internal Revenue Code of 1986, as amended, restricted stock and other incentive awards and rights to purchase shares of our common stock.

	The Option and Incentive Plan is administered by the Compensation Committee of the Board of Directors, which has the authority to select the individuals to whom awards will be granted, the number of shares, vesting terms, exercise price and term of each option grant. Generally, options have a four-year annual vesting term, an exercise price equal to the market value of the underlying shares at the grant date and a ten-year life from the date of grant.

	Warrants

	Associated with our previously outstanding long-term debt arrangements under the Deerfield credit facilities, we issued warrants to Deerfield to purchase 6,000,000 shares of common stock at an exercise price of $3.65 and warrants to purchase 6,000,000 shares of common stock at an exercise price of $4.19. The warrants contain the same terms, except for the lower per share exercise price. We valued the warrants at issuance based on a Black-Scholes option pricing model and then allocated a portion of the proceeds under the debt to the warrants based upon their relative fair values. The warrants were recorded in stockholders' deficit with the offset to debt discount. The debt discount was amortized using the effective interest method and recorded as interest expense in the accompanying statements of operations and comprehensive loss from the respective draw dates until June 10, 2013, when the Deerfield credit facilities were repaid and the recognition of the remaining debt discount was accelerated. The warrants are currently exercisable and expire on June 30, 2016.

	Controlled Equity Offering

	On March 27, 2013, we entered into a Sales Agreement with Cantor Fitzgerald & Co. ("Cantor"), pursuant to which we could sell up to $75 million in shares of our common stock from time to time through Cantor, acting as our sales agent, in an at-the-market offering. The Sales Agreement concluded in June 2014 upon completion of the sale of all shares available under the Sales Agreement. All sales of shares were made pursuant to an effective shelf registration statement on Form S-3 filed with the SEC. We paid Cantor a commission of approximately 2% of the aggregate gross proceeds we received from all sales of our common stock under the Sales Agreement.

	During the year ended June 30, 2014, we sold approximately 13.8 million shares of common stock at an average price of $5.43 per share, for gross proceeds of $75.0 million. Cantor earned commissions of $1.5 million relating to these sales.

SHAREBASED_COMPENSATION

SHARE-BASED COMPENSATION	12 Months Ended
	Jun. 30, 2014
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]	'
SHARE-BASED COMPENSATION	'
	SHARE-BASED COMPENSATION

	Total share-based compensation expense recorded for equity awards issued pursuant to the Option and Incentive Plan and for shares issued under the ESPP was $4.3 million, $3.4 million and $2.4 million for the fiscal years ended June 30, 2014, 2013 and 2012, respectively.

	We use the Black-Scholes option pricing model to estimate the fair value of our share-based awards. In applying this model, we use the following assumptions:

	•	Risk-free interest rate - We determine the risk-free interest rate by using a weighted average assumption equivalent to the expected term based on the U.S. Treasury constant maturity rate.

	•	Expected term - We estimate the expected term of our options based upon historical exercises and post-vesting termination behavior.

	•	Expected volatility - We estimate expected volatility using daily historical trading data of our common stock.

	•	Dividend yield - We have never paid dividends and currently have no plans to do so; therefore, no dividend yield is applied.
	The fair value of our option awards was estimated using the assumptions below, which yielded the following weighted average grant date fair values for the periods presented:


		Year Ended June 30,
		2014		2013		2012

	Risk-free interest rate	1.7% - 2.1%		0.8% - 1.2%		0.9% - 1.5%
	Expected option term in years	6.25		6.25		6.25
	Expected volatility	67.8% - 68.9%		66.0% - 67.5%		63.8% - 65.8%
	Dividend yield	0%		0%		0%
	Weighted-average grant date fair value	$2.91		$3.07		$2.04

	The following table summarizes our stock option activity under the Option and Incentive Plan for the year ended June 30, 2014:


		Number of			Weighted		Weighted Average Remaining Contractual Term (in years)	Aggregate Intrinsic Value (in thousands)
		Options			Average
					Exercise
					Price
	Outstanding at June 30, 2013	10,337,737			$	4.87

	Granted	2,454,244			$	4.63

	Exercised	(859,472	)		$	3.33

	Forfeited	(1,675,631	)		$	5.43

	Expired or canceled	(62,061	)		$	8.23

	Outstanding balance at June 30, 2014	10,194,817			$	4.84	7	$	4,656

	Vested and expected to vest at June 30, 2014	8,491,883			$	4.91	6.7	$	4,182

	Exercisable at June 30, 2014	4,712,643			$	5.27	4.9	$	2,931


	The aggregate intrinsic value in the above table is calculated as the difference between the closing price of our common stock at June 30, 2014, of $4.56 per share and the exercise price of the stock options that had strike prices below the closing price. The total intrinsic value of all options exercised during the years ended June 30, 2014, 2013 and 2012 was $2.0 million, $853 thousand and $78 thousand, respectively.

	As of June 30, 2014, there was approximately $8.6 million of total unrecognized compensation expense, including estimated forfeitures, related to the unvested stock options in the table above, which is expected to be recognized over a weighted average period of 3.0 years.

	Employee Stock Purchase Plan

	An aggregate of 4,650,000 shares of our common stock are reserved for issuance under the ESPP. The ESPP allows qualified employees (as defined in the ESPP) to purchase shares of our common stock at a price equal to 85% of the lower of (i) the closing price at the beginning of the offering period or (ii) the closing price at the end of the offering period. Effective each January 1, a new 12-month offering period begins that will end on December 31 of that year. However, if the closing stock price on July 1 is lower than the closing stock price on the preceding January 1, then the original 12-month offering period terminates, and the purchase rights under the original offering period roll forward into a new six-month offering period that begins July 1 and ends on December 31. As of June 30, 2014, we had 491,649 shares available for issuance under the ESPP. We issued 309,287, 524,296 and 443,651 shares under the ESPP during fiscal 2014, 2013 and 2012, respectively.

EMPLOYEE_BENEFIT_PLAN

EMPLOYEE BENEFIT PLAN	12 Months Ended
EMPLOYEE BENEFIT PLAN	Jun. 30, 2014
Compensation and Retirement Disclosure [Abstract]	'
EMPLOYEE BENEFIT PLAN	'
	EMPLOYEE BENEFIT PLAN

	Employee Savings Plan

	Array has a 401(k) plan that allows participants to contribute from 1% to 60% of their salary, subject to eligibility requirements and annual IRS limits. Array matches up to 4% of employee contributions on a discretionary basis as determined by our Board of Directors. Company contributions are fully vested after four years of employment. We paid matching contributions of approximately $1.2 million, $820 thousand and $1.0 million during the years ended June 30, 2014, 2013 and 2012, respectively.

RESTRUCTURING_CHARGES

RESTRUCTURING CHARGES	12 Months Ended
RESTRUCTURING CHARGES	Jun. 30, 2014
Restructuring and Related Activities [Abstract]	'
RESTRUCTURING CHARGES	'
	RESTRUCTURING CHARGES

	On August 5, 2013, we implemented a 20% reduction in our workforce and the affected employees were immediately notified. The reduction in force supports our strategy to fund our development organization with strategic collaborations and to focus our resources to progress our hematology and oncology programs to later stage development. The actions associated with the reductions were substantially completed during the first quarter of fiscal 2014 and, as a result of the reductions, we recorded a one-time restructuring charge of $2.8 million for termination benefits in the same period. Of this charge, $2.2 million was recorded in research and development for proprietary programs and $602 thousand was recorded in general and administrative expense. The restructuring charge is associated with cash payments of $2.6 million and $194 thousand made during the first quarter and second quarter, respectively, of fiscal 2014.

	We continue to evaluate our facility needs and may decide to vacate or abandon additional space in Longmont and/or Boulder. If we do so, or conclude it is more likely than not that we will vacate the remaining space within a defined period, we may recognize additional impairment charges relating to the remaining book value of any improvements. If we conclude that it is more likely than not that we will vacate the remaining space within a defined period, the remaining net book value at the time will be evaluated for impairment. In addition, if we do vacate or abandon the remaining space, we will record as an additional expense the present value of future rent payments, less applicable deferred rent amounts, to the extent it exceeds potential sublet income.

INCOME_TAXES

INCOME TAXES	12 Months Ended
	Jun. 30, 2014
Income Tax Disclosure [Abstract]	'
INCOME TAXES	'
	INCOME TAXES

	We have incurred net losses since inception, and we did not record an income tax provision or benefit during fiscal 2014, 2013 and 2012.

	A reconciliation of income taxes at the statutory federal income tax rate to net income taxes included in the accompanying statements of operations and comprehensive loss is set forth in the following table:



		Year Ended June 30,
		2014		2013			2012

	U.S. federal income tax expense at the statutory rate	34	%	34	%		34	%
	Interest expense disallowed under Sec.163(l)	0		(5.0	)		(15.6	)

	Available research and experimentation tax credits	2		5.7			12.9

	Stock-based compensation	(1.2	)	(3.8	)		(2.6	)
	(Gain)/loss on early prepayment of debt	0		(6.1	)		(1.4	)

	FIN 48 reserve releases	(0.3	)	(0.7	)		7.3

	Rate change	0		(0.8	)		(2.2	)

	Effect of other permanent differences	(0.1	)	0.2			0

	State income taxes, net of federal taxes	3.1		2			1.4

	Valuation allowance	(37.5	)	(25.5	)		(33.8	)
	Total	0	%	0	%		0	%
	Deferred tax assets and liabilities reflect the net tax effects of net operating losses, credit carryforwards and temporary differences between the carrying amounts of assets and liabilities for financial reporting purposes and amounts used for income tax purposes.

	The components of our deferred tax assets and liabilities are (in thousands):


		June 30,
		2014			2013
	Current deferred tax assets, gross
	Accrued benefits	$	2,402		$	2,725

	Inventory reserve	1,514			1,203

	Total current deferred tax assets	3,916			3,928

	Non-current deferred tax assets, gross
	Net operating loss carryforwards	196,997			162,791

	Capital loss carryforwards	6,095			6,094

	Research and experimentation credit carryforwards	28,558			27,060

	Deferred revenue	197			4,951

	Deferred rent	2,909			4,261

	Depreciation of property and equipment	7,666			6,885

	Loan costs on convertible senior notes	469			565

	Other	2,333			2,439

	Total non-current deferred tax assets	245,224			215,046

	Total deferred tax assets	249,140			218,974

Long-term deferred tax liability
Discount on convertible senior notes	15,905			17,734

Total long-term deferred tax liability	15,905			17,734

Deferred tax assets, net of deferred tax liability	233,235			201,240

Valuation allowance	(233,235		)	(201,240		)
Deferred tax assets, net of valuation allowance	$	—		$	—


Based upon the level of historical taxable loss and projections of future taxable losses over the periods in which the deferred tax assets are deductible, management believes it is more likely than not that we will not realize the benefits of these deductible differences and accordingly has established a full valuation allowance as of June 30, 2014 and 2013 against our deferred tax assets.

Future realization depends on the future earnings of Array, if any, the timing and amount of which are uncertain as of June 30, 2014. In the future, should management conclude that it is more likely than not that the deferred tax assets are partially or fully realizable, the valuation allowance would be reduced to the extent of such expected realization and the amount would be recognized as a deferred income tax benefit in our statements of operations and comprehensive loss.

Certain tax benefits from employee stock option exercises are included in the deferred tax asset balances as of June 30, 2014 and 2013 as a component of our net operating loss carryforwards. The deferred tax asset balances as of June 30, 2014 and 2013 do not include excess tax benefits from stock option exercises of approximately $4.6 million and $4.5 million for fiscal 2014 and 2013, respectively. Equity will be increased if and when management determines that it is more likely than not that such excess tax benefits will ultimately be realized.

As of June 30, 2014, we had available total net operating loss carryforwards of approximately $545.3 million, which expire in the years 2020 through 2033, and federal research and experimentation credit carryforwards of $31.5 million, which expire in the years 2022 through 2033. Capital loss carryforwards begin to expire in 2015.

The Tax Reform Act of 1986 and certain state tax statutes limit the utilization of net operating loss and tax credit carryforwards to offset future taxable income and tax, and may therefore result in the expiration of a portion of those carryforwards before they are utilized, if there has been a "change of ownership" as described in Section 382 of the Internal Revenue Code, and under similar state provisions. During fiscal 2012, we conducted a study to determine whether a change of ownership event occurred in prior fiscal years that would limit the net operating losses available to fully offset our taxable income. Based on our analysis, approximately $40 thousand of our net operating losses as of the year ended June 30, 2011, may not be used to offset taxable income. We have provided a valuation allowance against the entire amount of our net operating loss and tax credit carryforwards. We will continue to evaluate past and future events that could limit our ability to utilize our net operating losses and tax credit carryforwards in future years.

We follow a comprehensive model for recognizing, measuring, presenting and disclosing uncertain tax positions taken or expected to be taken on a tax return. Tax positions must initially be recognized in the financial statements when it is more likely than not that the position will be sustained upon examination by the tax authorities. Such tax positions must initially and subsequently be measured as the largest amount of tax benefit that has a greater than 50% likelihood of being realized upon ultimate settlement with the tax authority assuming full knowledge of the position and relevant facts.

The cumulative effect of accounting for tax contingencies in this manner has been recorded in deferred tax assets, net of the full valuation allowance, which resulted in no liability being recorded on our accompanying balance sheets. The total amount of unrecognized tax benefits as of June 30, 2014 and 2013 are (in thousands):



	Year Ended June 30,
	2014			2013

Balance at beginning of year	$	3,428		$	2,968

Additions based on tax positions related to the current year	712			915

Additions for tax positions of prior year	—			(2		)

Reductions for tax positions of prior year	(464		)	(453		)
Balance at end of year	$	3,676		$	3,428


There are open statutes of limitations for taxing authorities in federal and state jurisdictions to audit our tax returns from inception of Array. Our policy is to account for income tax related interest and penalties in income tax expense in the accompanying statements of operations and comprehensive loss. There have been no income tax related interest or penalties assessed or recorded. Because we have provided a full valuation allowance on all of our deferred tax assets, the adoption of accounting for tax contingencies had no impact on our effective tax rate.

SELECTED_QUARTERLY_FINANCIAL_D

SELECTED QUARTERLY FINANCIAL DATA (UNAUDITED)	12 Months Ended
	Jun. 30, 2014
Quarterly Financial Information Disclosure [Abstract]	'
SELECTED QUARTERLY FINANCIAL DATA (UNAUDITED)	'
	SELECTED QUARTERLY FINANCIAL DATA (UNAUDITED)

	The tables below summarize our unaudited quarterly operating results for the fiscal years ended June 30, 2014 and 2013 (dollars in thousands, except per share data):



	Fiscal Year Ended June 30, 2014	First Quarter			Second Quarter			Third Quarter			Fourth Quarter
	Revenue	$	14,228		$	14,066		$	7,773		$	6,011

	Research and development for proprietary programs	$	11,704		$	9,487		$	14,131		$	14,502

	Total operating expenses	$	27,541		$	28,069		$	30,292		$	31,794

	Net loss	$	(15,680	)	$	(16,408	)	$	(24,932	)	$	(28,237	)
	Weighted average shares outstanding – basic and diluted	117,509			123,921			125,471			126,815

	Net loss per share – basic and diluted	$	(0.13	)	$	(0.13	)	$	(0.20	)	$	(0.22	)



	Fiscal Year Ended June 30, 2013	First Quarter			Second Quarter			Third Quarter			Fourth Quarter
	Revenue	$	15,833		$	18,377		$	9,955		$	25,415

	Research and development for proprietary programs	$	13,534		$	13,941		$	15,105		$	16,840

	Total operating expenses	$	24,853		$	26,460		$	28,730		$	29,079

	Net loss	$	(11,768	)	$	(10,931	)	$	(21,594	)	$	(17,649	)
	Weighted average shares outstanding – basic and diluted	92,606			105,403			116,665			116,792

	Net loss per share – basic and diluted	$	(0.13	)	$	(0.10	)	$	(0.19	)	$	(0.15	)

	The net loss per share amounts above may not sum to the annual amounts presented in our accompanying statements of operations and comprehensive loss due to rounding.

SUBSEQUENT_EVENT

SUBSEQUENT EVENT	12 Months Ended
SUBSEQUENT EVENT	Jun. 30, 2014
Subsequent Events [Abstract]	'
SUBSEQUENT EVENT	'
	SUBSEQUENT EVENT

	All of the shares of preferred stock held by Array and received under our Drug Discovery Collaboration Agreement with Loxo converted automatically into shares of common stock on July 31, 2014, the effective date of Loxo's initial public offering. Under the initial public offering, Loxo sold common stock to the public at a price of $13.00 per share. Array currently holds approximately 1.6 million shares of Loxo common stock, which represents an approximate 10% ownership interest in Loxo. We are subject to a typical underwriter's lockup period, after which we are eligible to sell our investment subject to the SEC's Rule 144 and other registration rights.

OVERVIEW_AND_BASIS_OF_PRESENTA1

OVERVIEW AND BASIS OF PRESENTATION (Policies)	12 Months Ended
	Jun. 30, 2014
Organization, Consolidation and Presentation of Financial Statements [Abstract]	'
Basis of Presentation	'
	Basis of Presentation

	The accompanying financial statements have been prepared in accordance with U.S. generally accepted accounting principles (“U.S. GAAP”) and include all adjustments necessary for the fair presentation of our financial position, results of operations and cash flows for the periods presented. Our management performed an evaluation of our activities through the date of filing of this Annual Report on Form 10-K, and concluded that there are no subsequent events, except as disclosed in Note 13 to these financial statements.
Use of Estimates	'
	Use of Estimates

	The preparation of financial statements in conformity with U.S. GAAP requires our management to make estimates and assumptions that affect the reported amounts of assets, liabilities, revenue and expenses, and related disclosure of contingent assets and liabilities. Management bases its estimates on our historical experience and on various other assumptions that we believe are reasonable under the circumstances. These estimates are the basis for our judgments about the carrying values of assets and liabilities, which in turn may impact our reported revenue and expenses. Our actual results could differ significantly from these estimates under different assumptions or conditions.

	We believe our financial statements are most significantly impacted by the following accounting estimates and judgments: (i) the identification of deliverables under collaboration and license agreements involving multiple elements and determining whether such deliverables are separable from other aspects of the contractual relationship; (ii) estimating the selling price of deliverables for the purpose of allocating arrangement consideration for revenue recognition; (iii) estimating the periods over which the allocated consideration for deliverables is recognized; (iv) estimating accrued outsourcing costs for clinical trials and preclinical testing; (v) estimating the fair value of non-marketable equity received from licensing transactions; and (vi) determination of fair value of the debt component for our convertible senior notes exclusive of the conversion feature.
Fair Value Measurements	'
	Fair Value Measurements

	We follow accounting guidance on fair value measurements for financial instruments measured on a recurring basis, as well as for certain assets and liabilities that are initially recorded at their estimated fair values. Fair value is defined as the exit price, or the amount that would be received from selling an asset or paid to transfer a liability in an orderly transaction between market participants at the measurement date. We use the following three-level hierarchy that maximizes the use of observable inputs and minimizes the use of unobservable inputs to value our financial instruments:

	•	Level 1: Observable inputs such as unadjusted quoted prices in active markets for identical instruments.

	•	Level 2: Quoted prices for similar instruments that are directly or indirectly observable in the marketplace.

	•	Level 3: Significant unobservable inputs which are supported by little or no market activity and that are financial instruments whose values are determined using pricing models, discounted cash flow methodologies, or similar techniques, as well as instruments for which the determination of fair value requires significant judgment or estimation.

	Financial instruments measured at fair value are classified in their entirety based on the lowest level of input that is significant to the fair value measurement. Our assessment of the significance of a particular input to the fair value measurement in its entirety requires us to make judgments and consider factors specific to the asset or liability. The use of different assumptions and/or estimation methodologies may have a material effect on estimated fair values. Accordingly, the fair value estimates disclosed or initial amounts recorded may not be indicative of the amount that we or holders of the instruments could realized in a current market exchange.
	The carrying amounts of cash equivalents and marketable securities approximate their fair value based upon quoted market prices. Certain of our financial instruments are not measured at fair value on a recurring basis, but are recorded at amounts that approximate their fair value due to their liquid or short-term nature, such as cash, accounts receivable and payable, and other financial instruments in current assets or current liabilities.
Cash and Cash Equivalents and Concentration of Credit Risk	'
	Cash and Cash Equivalents and Concentration of Credit Risk

	Cash and cash equivalents consist of cash and short-term, highly-liquid financial instruments that are readily convertible to cash and have maturities of 90 days or less from the date of purchase. They may consist of money market funds, commercial paper, U.S. government agency obligations and corporate notes and bonds with high credit quality. We currently maintain all cash in several institutions in the U.S. Balances at these institutions may exceed Federal Deposit Insurance Corporation insured limits.
Marketable Securities	'
	Marketable Securities

	We have designated our marketable securities as of each balance sheet date as available-for-sale securities and account for them at their respective fair values. Marketable securities are classified as short-term or long-term based on the nature of the securities and their availability to meet current operating requirements. Marketable securities that are readily available for use in current operations are classified as short-term available-for-sale securities and are reported as a component of current assets in the accompanying balance sheets. Marketable securities that are not considered available for use in current operations are classified as long-term available-for-sale securities and are reported as a component of long-term assets in the accompanying balance sheets.

	Securities that are classified as available-for-sale are carried at fair value, including accrued interest, with temporary unrealized gains and losses reported as a component of stockholders' deficit until their disposition. We review all available-for-sale securities at each period end to determine if they remain available-for-sale based on our then current intent and ability to sell the security if it is required to do so. The cost of securities sold is based on the specific identification method.

	All of our marketable securities are subject to a periodic impairment review. We recognize an impairment charge when a decline in the fair value of our investments below the cost basis is judged to be other-than-temporary.
Property and Equipment	'
	Property and Equipment

	Property and equipment are stated at historical cost less accumulated depreciation and amortization. Additions and improvements are capitalized. Certain costs to internally develop software are also capitalized. Maintenance and repairs are expensed as incurred.

	Depreciation and amortization are computed on the straight-line method based on the following estimated useful lives:


	Furniture and fixtures	7 years
	Equipment	5 years
	Computer hardware and software	3 years

	We depreciate leasehold improvements associated with operating leases over the shorter of the expected useful life of the improvements or the remaining lease term.

	The carrying value for property and equipment is reviewed for impairment at least annually and when events or changes in circumstances indicate that the carrying value of the assets may not be recoverable. In addition, we continue to evaluate our facility needs and may decide to vacate or abandon a portion of one or more of our locations. If we do so, or conclude that we will vacate or abandon space within a defined period, we may recognize impairment charges relating to the remaining book value of any improvements and record as an additional expense the present value of future rent payments, less applicable deferred rent amounts, to the extent it exceeds potential sublet income.
Equity Investments	'
	Equity Investments

	From time to time, we may enter into collaboration and license agreements under which we receive an equity interest as consideration for all or a portion of up-front, license or other fees under the terms of the agreement. We report equity securities received from non-publicly traded companies in which we do not exercise a significant or controlling interest at cost in other long-term assets in the accompanying balance sheets. We monitor our investments for impairment at least annually, and consider events or changes in circumstances we know of that may have a significant adverse effect on the fair value. We make appropriate reductions in the carrying value if it is determined that an impairment has occurred, based primarily on the financial condition and near and long-term prospects of the issuer. We do not report the fair value of our equity investments because it is not practical to do so.
Accrued Outsourcing Costs	'
	Accrued Outsourcing Costs

	Substantial portions of our preclinical studies and clinical trials are performed by third-party laboratories, medical centers, contract research organizations and other vendors (collectively "CROs"). These CROs generally bill monthly or quarterly for services performed, or bill based upon milestone achievement. For preclinical studies, we accrue expenses based upon estimated percentage of work completed and the contract milestones remaining. For clinical studies, expenses are accrued based upon the number of patients enrolled and the duration of the study. We monitor patient enrollment, the progress of clinical studies and related activities to the extent possible through internal reviews of data reported to us by the CROs, correspondence with the CROs and clinical site visits. Our estimates depend on the timeliness and accuracy of the data provided by the CROs regarding the status of each program and total program spending. We periodically evaluate the estimates to determine if adjustments are necessary or appropriate based on information we receive.
Convertible Senior Notes	'
	Convertible Senior Notes

	Our 3.00% convertible senior notes due 2020 are accounted for in accordance with Financial Accounting Standards Board ("FASB") Accounting Standards Codification (“ASC”) 470-20, Debt – Debt with Conversion and Other Options. ASC 470-20 requires the issuer of convertible debt that may be settled in shares or cash upon conversion at the issuer's option, such as our notes, to account for the liability (debt) and equity (conversion option) components separately. The value assigned to the debt component is the estimated fair value, as of the issuance date, of a similar debt instrument without the conversion option. The amount of the equity component (and resulting debt discount) is calculated by deducting the fair value of the liability component from the principal amount of the convertible debt instrument. The resulting debt discount is amortized as additional non-cash interest expense over the expected life of the notes utilizing the effective interest method. Although ASC 470 has no impact on our actual past or future cash flows, it requires us to record non-cash interest expense as the debt discount is amortized.
Operating Leases	'
	Operating Leases

	We have negotiated certain landlord/tenant incentives and rent holidays and escalations in the base price of rent payments under our operating leases. For purposes of determining the period over which these amounts are recognized or amortized, the initial term of an operating lease includes the "build-out" period of leases, where no rent payments are typically due under the terms of the lease and includes additional terms pursuant to any options to extend the initial term if it is more likely than not that we will exercise such options. We recognize rent holidays and rent escalations on a straight-line basis over the initial lease term. The landlord/tenant incentives are recorded as an increase to deferred rent in the accompanying balance sheets and are amortized on a straight-line basis over the initial lease term. We have also entered into two sale-leaseback transactions for our facilities in Boulder and Longmont, Colorado, where the consideration received from the landlord was recorded as an increase to deferred rent in the accompanying balance sheets and is amortized on a straight-line basis over the lease term. Deferred rent balances are classified as short-term or long-term in the accompanying balance sheets based upon the period when reversal of the liability is expected to occur.
Share-Based Compensation	'
	Share-Based Compensation

	Share-based compensation awards include stock options granted under our Amended and Restated Stock Option and Incentive Plan and purchases of common stock by our employees at a discount to the market price under our Amended and Restated Employee Stock Purchase Plan ("ESPP"). We use the Black-Scholes option pricing model to determine the grant date fair value of stock options and ESPP awards. The determination of the fair value of share-based awards using an option pricing model is affected by our stock price, as well as assumptions regarding a number of complex and subjective variables. Share-based compensation expense is recognized on a straight-line basis over the requisite service period for each award. Further, compensation expense recognized in our statement of operations and comprehensive loss for stock options is reduced for estimated forfeitures, which are based on historical experience and are revised in subsequent periods if actual forfeitures differ from our estimates.
Revenue Recognition	'
	Revenue Recognition

	We recognize revenue for the performance of services or the shipment of products when each of the following four criteria is met: (i) persuasive evidence of an arrangement exists; (ii) products are delivered or as services are rendered; (iii) the sales price is fixed or determinable; and (iv) collectability is reasonably assured.

	We follow ASC 605-25, Revenue Recognition – Multiple-Element Arrangements and ASC 808, Collaborative Arrangements, if applicable, to determine the recognition of revenue under our collaborative research, development and commercialization agreements. The terms of these agreements generally contain multiple elements, or deliverables, which may include (i) grants of licenses, or options to obtain licenses, to our intellectual property, (ii) research and development services, (iii) drug product manufacturing, and/or (iv) participation on joint research and/or joint development committees. The payments we may receive under these arrangements typically include one or more of the following: non-refundable, up-front license fees; option exercise fees; funding of research and/or development efforts; amounts due upon the achievement of specified objectives; and/or royalties on future product sales.

	ASC 605-25 provides guidance relating to the separability of deliverables included in an arrangement into different units of accounting and the allocation of arrangement consideration to the units of accounting. The evaluation of multiple-element arrangements requires management to make judgments about (i) the identification of deliverables, (ii) whether such deliverables are separable from the other aspects of the contractual relationship, (iii) the estimated selling price of each deliverable, and (iv) the expected period of performance for each deliverable.

	To determine the units of accounting under a multiple-element arrangement, management evaluates certain separation criteria, including whether the deliverables have stand-alone value, based on the relevant facts and circumstances for each arrangement. Management then estimates the selling price for each unit of accounting and allocates the arrangement consideration to each unit utilizing the relative selling price method. The allocated consideration for each unit of accounting is recognized over the related obligation period in accordance with the applicable revenue recognition criteria.

	If there are deliverables in an arrangement that are not separable from other aspects of the contractual relationship, they are treated as a combined unit of accounting, with the allocated revenue for the combined unit recognized in a manner consistent with the revenue recognition applicable to the final deliverable in the combined unit. Payments received prior to satisfying the relevant revenue recognition criteria are recorded as deferred revenue in the accompanying balance sheets and recognized as revenue when the related revenue recognition criteria are met.

	We typically receive non-refundable, up-front payments when licensing our intellectual property, which often occurs in conjunction with a research and development agreement. When management believes that the license to our intellectual property has stand-alone value, we generally recognize revenue attributed to the license upon delivery provided that there are no future performance requirements for use of the license. When management believes that the license to our intellectual property does not have stand-alone value, we typically recognize revenue attributed to the license on a straight-line basis over the contractual or estimated performance period. When the performance period is not specifically identifiable from the agreement, we estimate the performance period based upon provisions contained within the agreement, such as the duration of the research or development term.

	Most of our agreements provide for non-refundable milestone payments. We recognize revenue that is contingent upon the achievement of a substantive milestone in its entirety in the period in which the milestone is achieved. A milestone is considered substantive when the consideration payable to us for such milestone (i) is consistent with our performance necessary to achieve the milestone or the increase in value to the collaboration resulting from our performance, (ii) relates solely to our past performance and (iii) is reasonable relative to all of the other deliverables and payments within the arrangement. In making this assessment, we consider all facts and circumstances relevant to the arrangement, including factors such as the scientific, regulatory, commercial and other risks that must be overcome to achieve the milestone, the level of effort and investment required to achieve the milestone and whether any portion of the milestone consideration is related to future performance or deliverables.

	For payments payable on achievement of milestones that do not meet all of the conditions to be considered substantive, we recognize a portion of the payment as revenue when the specific milestone is achieved, and the contingency is removed, based on the applicable percentage earned of the estimated research or development effort, or other performance obligations that have elapsed, to the total estimated research and/or development effort attributable to the milestone. In other cases, when a non-substantive milestone payment is attributed to our future research or development obligations, we recognize the revenue on a straight-line basis, or other appropriate method, over the estimated remaining research or development effort. Other contingent event-based payments for which payment is either contingent solely upon the passage of time or the result of our partner's or collaborator's performance are recognized when earned.

	We periodically review the estimated performance periods under each of our agreements that provide for non-refundable up-front payments, license fees or milestone payments. We adjust the periods over which revenue should be recognized when appropriate to reflect changes in assumptions relating to the estimated performance periods. We could accelerate revenue recognition in the event of early termination of programs or if our expectations change. Alternatively, we could decelerate revenue recognition if programs are extended or delayed. While such changes to our estimates have no impact on our reported cash flows, the amount of revenue recorded in future periods could be materially impacted.
Income Taxes	'
	Income Taxes

	We account for income taxes using the asset and liability method. We recognize the amount of income taxes payable (refundable) for the year as current income tax provision (benefit) and record a deferred income tax provision (benefit) based on changes in deferred tax assets and liabilities. Deferred tax assets and liabilities are determined based on the difference between the financial statement carrying value and the tax basis of assets and liabilities and, using enacted tax rates in effect, reflect the expected effect these differences would have on future taxable income, if any. Valuation allowances are recorded to reduce the amount of deferred tax assets when management cannot conclude it is more likely than not that some or all of the deferred tax assets will be realized. Such allowances are based upon available objective evidence, the expected reversal of temporary differences and projections of future taxable income.
	Our policy is to account for income tax related interest and penalties in income tax expense in the accompanying statements of operations and comprehensive loss.
Net Loss per Share	'
	Net Loss per Share

	Basic net loss per share is computed by dividing net loss for the period by the weighted average number of common shares outstanding during the period. Diluted net loss per share reflects the additional dilution from potential issuances of common stock, such as stock issuable pursuant to the exercise of stock options, as well as from the possible conversion of our convertible senior notes and exercise of outstanding warrants. The treasury stock method is used to calculate the potential dilutive effect of these common stock equivalents. Potentially dilutive shares are excluded from the computation of diluted net loss per share when their effect is anti-dilutive. As a result of our net losses for all periods presented, all potentially dilutive securities were anti-dilutive and have been excluded from the computation of diluted net loss per share.
Balance Sheet Presentation of Co-Development Arrangements	'
	We record a receivable in accounts receivables on the balance sheet for the amounts due from Novartis for the reimbursement of our development costs in excess of the annual cap. We record expense in cost of partnered programs on the statement of operations and comprehensive loss for our share of the combined development costs and accrue these costs on our balance sheet in co-development liability.
Uncertain Tax Positions	'
	We follow a comprehensive model for recognizing, measuring, presenting and disclosing uncertain tax positions taken or expected to be taken on a tax return. Tax positions must initially be recognized in the financial statements when it is more likely than not that the position will be sustained upon examination by the tax authorities. Such tax positions must initially and subsequently be measured as the largest amount of tax benefit that has a greater than 50% likelihood of being realized upon ultimate settlement with the tax authority assuming full knowledge of the position and relevant facts.

OVERVIEW_AND_BASIS_OF_PRESENTA2

OVERVIEW AND BASIS OF PRESENTATION (Tables)	12 Months Ended
	Jun. 30, 2014
Organization, Consolidation and Presentation of Financial Statements [Abstract]	'
Schedule of estimated useful lives of property and equipment	'
	Depreciation and amortization are computed on the straight-line method based on the following estimated useful lives:


	Furniture and fixtures	7 years
	Equipment	5 years
	Computer hardware and software	3 years
	Property and equipment, net consists of the following (in thousands):


		June 30,
		2014				2013

	Furniture and fixtures	$	3,421			$	3,396

	Equipment	40,150				40,183

	Computer hardware and software	14,705				13,552

	Leasehold improvements	32,171				31,406

	Property and equipment, gross	90,447				88,537

	Less: accumulated depreciation and amortization	(82,290		)		(78,488		)
	Property and equipment, net	$	8,157			$	10,049

Schedule of partners that contributed greater than 10% of total revenue	'
	The following significant partners contributed greater than 10% of our total revenue during at least one of the periods set forth below. The revenue from these partners as a percentage of total revenue was as follows:


		Year Ended June 30,
		2014			2013			2012

	Novartis International Pharmaceutical Ltd.	28.6	%		25.5	%		16.2	%
	Loxo Oncology, Inc.	23.1			—			—

	AstraZeneca AB	12.1			0.2			—

	Celgene	8.9			20.6			6.9

	Genentech, Inc.	8.5			11			40.8

	Oncothyreon Inc.	8.2			14.4			—

	Amgen Inc.	—			16			34.2

		89.4	%		87.7	%		98.1	%
Schedule of revenue by geographic area based on the country in which partners are located	'
	The following table details revenue by geographic area based on the country in which our partners are located (in thousands):


		Year Ended June 30,
		2014				2013				2012

	North America	$	24,757			$	51,608			$	70,905

	Europe	17,153				17,969				13,987

	Asia Pacific	168				3				243

		$	42,078			$	69,580			$	85,135

MARKETABLE_SECURITIES_Tables

MARKETABLE SECURITIES (Tables)	12 Months Ended
	Jun. 30, 2014
Marketable Securities [Abstract]	'
Schedule of marketable securities	'
	Marketable securities consisted of the following as of June 30, 2014 (in thousands):


				Gross		Gross
		Amortized		Unrealized		Unrealized			Fair
		Cost		Gains		Losses			Value
	Short-term available-for-sale securities:
	U.S. treasury securities	$	42,184	$	2	$	(1	)	$	42,185

	Mutual fund securities	222		—		—			222

		42,406		2		(1		)	42,407

	Long-term available-for-sale securities:
	Mutual fund securities	640		—		—			640

		640		—		—			640

	Total	$	43,046	$	2	$	(1	)	$	43,047


	Marketable securities consisted of the following as of June 30, 2013 (in thousands):


				Gross		Gross
		Amortized		Unrealized		Unrealized			Fair
		Cost		Gains		Losses			Value
	Short-term available-for-sale securities:
	U.S. treasury securities	$	47,130	$	—	$	(2	)	$	47,128

	Mutual fund securities	377		—		—			377

		47,507		—		(2		)	47,505

	Long-term available-for-sale securities:
	Mutual fund securities	465		—		—			465

		465		—		—			465

	Total	$	47,972	$	—	$	(2	)	$	47,970

Schedule of fair value measurement categories of marketable securities	'
	The estimated fair value of our marketable securities was classified into fair value measurement categories as follows (in thousands):


		June 30,
		2014		2013

	Quoted prices in active markets for identical assets (Level 1)	$	43,047	$	47,970

	Quoted prices for similar assets observable in the marketplace (Level 2)	—		—

	Significant unobservable inputs (Level 3)	—		—

	Total	$	43,047	$	47,970

Schedule of amortized cost and estimated fair value of available-for-sale securities by contractual maturity	'
	As of June 30, 2014, the amortized cost and estimated fair value of available-for-sale securities by contractual maturity were as follows (in thousands):


		Amortized		Fair
		Cost		Value

	Due in one year or less	$	42,406	$	42,407

	Due in one year to three years	640		640

	Total	$	43,046	$	43,047

PROPERTY_AND_EQUIPMENT_NET_Tab

PROPERTY AND EQUIPMENT, NET (Tables)	12 Months Ended
	Jun. 30, 2014
Property, Plant and Equipment [Abstract]	'
Schedule of property and equipment, net	'
	Depreciation and amortization are computed on the straight-line method based on the following estimated useful lives:


	Furniture and fixtures	7 years
	Equipment	5 years
	Computer hardware and software	3 years
	Property and equipment, net consists of the following (in thousands):


		June 30,
		2014			2013

	Furniture and fixtures	$	3,421		$	3,396

	Equipment	40,150			40,183

	Computer hardware and software	14,705			13,552

	Leasehold improvements	32,171			31,406

	Property and equipment, gross	90,447			88,537

	Less: accumulated depreciation and amortization	(82,290		)	(78,488		)
	Property and equipment, net	$	8,157		$	10,049

COLLABORATION_AND_LICENSE_AGRE1

COLLABORATION AND LICENSE AGREEMENTS (Tables)	12 Months Ended
	Jun. 30, 2014
Collaboration and License Agreements [Abstract]	'
Schedule of deferred revenue	'
	Deferred revenue consisted of the following (in thousands):


		June 30,
		2014			2013

	Celgene	$	7,258		$	—

	Biogen Idec	1,218			—

	Loxo Oncology, Inc.	625			—

	Genentech, Inc.	367			2,300

	Novartis International Pharmaceutical Ltd.	—			12,053

	Other partners	78			—

	Total deferred revenue	9,546			14,353

	Less: Current portion	(6,193		)	(14,353		)
	Deferred revenue, long-term portion	$	3,353		$	—

LONGTERM_DEBT_Tables

LONG-TERM DEBT (Tables)	12 Months Ended
	Jun. 30, 2014
Debt Disclosure [Abstract]	'
Schedule of long-term debt	'
	Long-term debt consists of the following (in thousands):


		June 30,
		2014			2013

	Comerica term loan	$	14,550		$	14,550

	Convertible senior notes	132,250			132,250

	Long-term debt, gross	146,800			146,800

	Less: Unamortized debt discount	(42,848		)	(47,779		)
	Long-term debt, net	$	103,952		$	99,021

Schedule of loss on prepayment of debt	'
	Ultimately, the remaining outstanding balances of debt discount and debt transaction fees were written off upon repayment of the credit facilities as follows (in thousands):


		Year Ended June 30,
		2013			2012

	Write off proportional value or remaining balance of the debt discount	$	(10,898	)	$	(887	)
	Write off proportional value or remaining balance of the unamortized debt issuance costs	(720		)	(55		)

	Fair value adjustment for, or write off of, the embedded derivatives	421			—

	Loss on prepayment of long-term debt, net	$	(11,197	)	$	(942	)
Schedule of interest expense	'
	The following table shows the details of our interest expense for all of our debt arrangements outstanding during the periods presented, including contractual interest, and amortization of debt discount, debt issuance costs and loan transaction fees that were charged to interest expense (in thousands):


		Year Ended June 30,
		2014			2013			2012
	Comerica Term Loan
	Simple interest	$	479		$	483		$	489

	Amortization of fees paid for letters of credit	48			107			108

	Total interest expense on the Comerica term loan	527			590			597


	Convertible Senior Notes
	Contractual interest	3,979			221			—

	Amortization of debt discount	4,932			259			—

	Amortization of debt issuance costs	278			14			—

	Total interest expense on the convertible senior notes	9,189			494			—


	Deerfield Credit Facilities
	Simple interest	—			6,078			6,492

	Amortization of debt discounts and transaction fees	—			4,331			4,419

	Change in fair value of the embedded derivatives	—			(235		)	116

	Total interest expense on the Deerfield credit facilities	—			10,174			11,027

	Total interest expense	$	9,716		$	11,258		$	11,624

Schedule of principal payments required for long-term debt	'
	We are required to make principal payments for our long-term debt as follows during the fiscal years ending June 30 (in thousands):


		Principal Due

	2015	$	—

	2016	—

	2017	—

	2018	14,550

	2019	—

	Thereafter	132,250

		$	146,800

COMMITMENTS_AND_CONTINGENCIES_

COMMITMENTS AND CONTINGENCIES (Tables)	12 Months Ended
	Jun. 30, 2014
Commitments and Contingencies Disclosure [Abstract]	'
Schedule of future minimum rental commitments	'
	Future minimum rental commitments for our operating leases, by fiscal year and in the aggregate, as of June 30, 2014, are (in thousands):


			Rental Payments

	2015		$	8,316

	2016		8,338

	2017		368

	2018		—

	2019		—

	Thereafter		—

			$	17,022

Schedule of rent expense	'
	Rent expense under these agreements follows (dollars in thousands):


		Year Ended June 30,
		2014			2013			2012

	Cash paid for rent	$	8,878		$	8,625		$	8,549

	Deferred rent credits	(3,645		)	(3,489		)	(3,332		)
	Rent expense, net	$	5,233		$	5,136		$	5,217

SHAREBASED_COMPENSATION_Tables

SHARE-BASED COMPENSATION (Tables)	12 Months Ended
	Jun. 30, 2014
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]	'
Schedule of fair value assumptions	'
	The fair value of our option awards was estimated using the assumptions below, which yielded the following weighted average grant date fair values for the periods presented:


		Year Ended June 30,
		2014		2013		2012

	Risk-free interest rate	1.7% - 2.1%		0.8% - 1.2%		0.9% - 1.5%
	Expected option term in years	6.25		6.25		6.25
	Expected volatility	67.8% - 68.9%		66.0% - 67.5%		63.8% - 65.8%
	Dividend yield	0%		0%		0%
	Weighted-average grant date fair value	$2.91		$3.07		$2.04
Summary of stock option activity	'
	The following table summarizes our stock option activity under the Option and Incentive Plan for the year ended June 30, 2014:


		Number of			Weighted		Weighted Average Remaining Contractual Term (in years)	Aggregate Intrinsic Value (in thousands)
		Options			Average
					Exercise
					Price
	Outstanding at June 30, 2013	10,337,737			$	4.87

	Granted	2,454,244			$	4.63

	Exercised	(859,472	)		$	3.33

	Forfeited	(1,675,631	)		$	5.43

	Expired or canceled	(62,061	)		$	8.23

	Outstanding balance at June 30, 2014	10,194,817			$	4.84	7	$	4,656

	Vested and expected to vest at June 30, 2014	8,491,883			$	4.91	6.7	$	4,182

	Exercisable at June 30, 2014	4,712,643			$	5.27	4.9	$	2,931

INCOME_TAXES_Tables

INCOME TAXES (Tables)	12 Months Ended
	Jun. 30, 2014
Income Tax Disclosure [Abstract]	'
Schedule of reconciliation of income taxes at the statutory federal income tax rate to net income taxes	'
	A reconciliation of income taxes at the statutory federal income tax rate to net income taxes included in the accompanying statements of operations and comprehensive loss is set forth in the following table:



		Year Ended June 30,
		2014			2013			2012

	U.S. federal income tax expense at the statutory rate	34	%		34	%		34	%
	Interest expense disallowed under Sec.163(l)	0			(5.0	)		(15.6	)

	Available research and experimentation tax credits	2			5.7			12.9

	Stock-based compensation	(1.2	)		(3.8	)		(2.6	)
	(Gain)/loss on early prepayment of debt	0			(6.1	)		(1.4	)

	FIN 48 reserve releases	(0.3	)		(0.7	)		7.3

	Rate change	0			(0.8	)		(2.2	)

	Effect of other permanent differences	(0.1	)		0.2			0

	State income taxes, net of federal taxes	3.1			2			1.4

	Valuation allowance	(37.5	)		(25.5	)		(33.8	)
	Total	0	%		0	%		0	%
Schedule of deferred tax assets and liabilities	'
	The components of our deferred tax assets and liabilities are (in thousands):


		June 30,
		2014				2013
	Current deferred tax assets, gross
	Accrued benefits	$	2,402			$	2,725

	Inventory reserve	1,514				1,203

	Total current deferred tax assets	3,916				3,928

	Non-current deferred tax assets, gross
	Net operating loss carryforwards	196,997				162,791

	Capital loss carryforwards	6,095				6,094

	Research and experimentation credit carryforwards	28,558				27,060

	Deferred revenue	197				4,951

	Deferred rent	2,909				4,261

	Depreciation of property and equipment	7,666				6,885

	Loan costs on convertible senior notes	469				565

	Other	2,333				2,439

	Total non-current deferred tax assets	245,224				215,046

	Total deferred tax assets	249,140				218,974

	Long-term deferred tax liability
	Discount on convertible senior notes	15,905				17,734

	Total long-term deferred tax liability	15,905				17,734

	Deferred tax assets, net of deferred tax liability	233,235				201,240

	Valuation allowance	(233,235		)		(201,240		)
	Deferred tax assets, net of valuation allowance	$	—			$	—

Schedule of unrecognized tax benefits	'
	The total amount of unrecognized tax benefits as of June 30, 2014 and 2013 are (in thousands):



		Year Ended June 30,
		2014				2013

	Balance at beginning of year	$	3,428			$	2,968

	Additions based on tax positions related to the current year	712				915

	Additions for tax positions of prior year	—				(2		)

	Reductions for tax positions of prior year	(464		)		(453		)
	Balance at end of year	$	3,676			$	3,428

SELECTED_QUARTERLY_FINANCIAL_D1

SELECTED QUARTERLY FINANCIAL DATA (UNAUDITED) (Tables)	12 Months Ended
	Jun. 30, 2014
Quarterly Financial Information Disclosure [Abstract]	'
Schedule of unaudited quarterly operating results	'
	The tables below summarize our unaudited quarterly operating results for the fiscal years ended June 30, 2014 and 2013 (dollars in thousands, except per share data):



	Fiscal Year Ended June 30, 2014	First Quarter			Second Quarter			Third Quarter			Fourth Quarter
	Revenue	$	14,228		$	14,066		$	7,773		$	6,011

	Research and development for proprietary programs	$	11,704		$	9,487		$	14,131		$	14,502

	Total operating expenses	$	27,541		$	28,069		$	30,292		$	31,794

	Net loss	$	(15,680	)	$	(16,408	)	$	(24,932	)	$	(28,237	)
	Weighted average shares outstanding – basic and diluted	117,509			123,921			125,471			126,815

	Net loss per share – basic and diluted	$	(0.13	)	$	(0.13	)	$	(0.20	)	$	(0.22	)



	Fiscal Year Ended June 30, 2013	First Quarter			Second Quarter			Third Quarter			Fourth Quarter
	Revenue	$	15,833		$	18,377		$	9,955		$	25,415

	Research and development for proprietary programs	$	13,534		$	13,941		$	15,105		$	16,840

	Total operating expenses	$	24,853		$	26,460		$	28,730		$	29,079

	Net loss	$	(11,768	)	$	(10,931	)	$	(21,594	)	$	(17,649	)
	Weighted average shares outstanding – basic and diluted	92,606			105,403			116,665			116,792

	Net loss per share – basic and diluted	$	(0.13	)	$	(0.10	)	$	(0.19	)	$	(0.15	)

OVERVIEW_AND_BASIS_OF_PRESENTA3

OVERVIEW AND BASIS OF PRESENTATION (Details) (USD $)

3 Months Ended

12 Months Ended

3 Months Ended

12 Months Ended

Jun. 30, 2014

Mar. 31, 2014

Dec. 31, 2013

Sep. 30, 2013

Jun. 30, 2013

Mar. 31, 2013

Dec. 31, 2012

Sep. 30, 2012

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2012

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2012

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2012

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2012

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2012

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2012

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2012

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2012

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2012

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2012

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2012

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2012

Sep. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jul. 31, 2013

Jun. 30, 2014

Jun. 30, 2013

Facility

Transaction

Sales

North America

Europe

Asia Pacific

Novartis International Pharmaceutical Ltd.

Loxo Oncology, Inc.

AstraZeneca AB

Celgene

Genentech, Inc.

Oncothyreon Inc.

Amgen Inc.

Loxo Oncology, Inc.

Furniture and fixtures

Equipment

Computer hardware and software

Comerica Loan and Security Agreement

Convertible Senior Notes, due 2020

Binimetinib

Loxo Oncology, Inc.

VentiRx Pharmaceuticals Inc

segment

Customer Concentration Risk

Sales

Accounts Receivable

Sales

Accounts Receivable

Sales

Line of credit

drug_trial

Preferred Stock

Facility

Customer Concentration Risk

Term loan

Long-term asset

Liquidity

Accumulated deficit

($717,936,000)

($632,679,000)

($717,936,000)

($632,679,000)

Net loss

-28,237,000

-24,932,000

-16,408,000

-15,680,000

-17,649,000

-21,594,000

-10,931,000

-11,768,000

-85,257,000

-61,942,000

-23,581,000

Number of drug trials

Amount of cash, cash equivalents and marketable securities that must be maintained at Comerica and approved outside accounts, or an amount equal to the entire outstanding debt balance with Comerica must be maintained at Comerica

22,000,000

Long-term debt, gross

146,800,000

14,550,000

Property and Equipment

Estimated useful life

'7 years

'5 years

'3 years

Number of facilities that may be vacated (or more)

Equity Investment

Estimated fair value of shares

4,500,000

Investment in preferred stock

4,500,000

1,500,000

Licenses revenue

4,500,000

Convertible Senior Notes

Stated interest rate

3.00%

Operating Leases

Number of sale-lease back transactions

Segments

Number of reportable segments

Concentration of Business Risks

Concentration risk percentage

89.40%

87.70%

98.10%

28.60%

25.50%

16.20%

75.00%

91.00%

23.10%

0.00%

12.10%

0.20%

0.00%

8.90%

20.60%

6.90%

8.50%

11.00%

40.80%

8.20%

14.40%

0.00%

15.00%

0.00%

16.00%

34.20%

Revenue

$6,011,000

$7,773,000

$14,066,000

$14,228,000

$25,415,000

$9,955,000

$18,377,000

$15,833,000

$42,078,000

$69,580,000

$85,135,000

$24,757,000

$51,608,000

$70,905,000

$17,153,000

$17,969,000

$13,987,000

$168,000

$3,000

$243,000

MARKETABLE_SECURITIES_Schedule

MARKETABLE SECURITIES (Schedule Of Marketable Securities) (Details) (USD $)	Jun. 30, 2014	Jun. 30, 2013
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013
Marketable securities	'	'
Amortized Cost	$43,046	$47,972
Gross Unrealized Gains	2	0
Gross Unrealized Losses	-1	-2
Fair value	43,047	47,970
Short-term investments	'	'
Marketable securities	'	'
Amortized Cost	42,406	47,507
Gross Unrealized Gains	2	0
Gross Unrealized Losses	-1	-2
Fair value	42,407	47,505
Short-term investments \| US Treasury Securities	'	'
Marketable securities	'	'
Amortized Cost	42,184	47,130
Gross Unrealized Gains	2	0
Gross Unrealized Losses	-1	-2
Fair value	42,185	47,128
Short-term investments \| Mutual fund securities	'	'
Marketable securities	'	'
Amortized Cost	222	377
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Fair value	222	377
Long-term investments	'	'
Marketable securities	'	'
Amortized Cost	640	465
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Fair value	640	465
Long-term investments \| Mutual fund securities	'	'
Marketable securities	'	'
Amortized Cost	640	465
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Fair value	$640	$465

MARKETABLE_SECURITIES_Schedule1

MARKETABLE SECURITIES (Schedule Of Fair Value Measurement Categories) (Details) (USD $)	Jun. 30, 2014	Jun. 30, 2013
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013
Fair value measurement categories	'	'
Fair value	$43,047	$47,970
Fair Value, Measurements, Recurring \| Quoted prices in active markets for identical assets (Level 1)	'	'
Fair value measurement categories	'	'
Fair value	43,047	47,970
Fair Value, Measurements, Recurring \| Quoted prices for similar assets observable in the marketplace (Level 2)	'	'
Fair value measurement categories	'	'
Fair value	0	0
Fair Value, Measurements, Recurring \| Significant unobservable inputs (Level 3)	'	'
Fair value measurement categories	'	'
Fair value	0	0
Fair Value, Measurements, Recurring \| Total fair value	'	'
Fair value measurement categories	'	'
Fair value	$43,047	$47,970

MARKETABLE_SECURITIES_Schedule2

MARKETABLE SECURITIES (Schedule of Amortized Cost And Estimated Fair Value) (Details) (USD $)	Jun. 30, 2014	Jun. 30, 2013
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013
Available-for-sale Securities, Debt Maturities, Amortized Cost Basis, Fiscal Year Maturity [Abstract]	'	'
Due in one year or less	$42,406	'
Due in one year to three years	640	'
Amortized Cost	43,046	'
Available-for-sale Securities, Debt Maturities, Fair Value, Fiscal Year Maturity [Abstract]	'	'
Due in one year or less	42,407	'
Due in one year to three years	640	'
Fair Value	$43,047	$47,970

PROPERTY_AND_EQUIPMENT_NET_Det

PROPERTY AND EQUIPMENT, NET (Details) (USD $)	Jun. 30, 2014	Jun. 30, 2013
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013
Property and equipment, net:	'	'
Property and equipment, gross	$90,447	$88,537
Less: accumulated depreciation and amortization	-82,290	-78,488
Property and equipment, net	8,157	10,049
Furniture and fixtures	'	'
Property and equipment, net:	'	'
Property and equipment, gross	3,421	3,396
Equipment	'	'
Property and equipment, net:	'	'
Property and equipment, gross	40,150	40,183
Computer hardware and software	'	'
Property and equipment, net:	'	'
Property and equipment, gross	14,705	13,552
Leasehold improvements	'	'
Property and equipment, net:	'	'
Property and equipment, gross	$32,171	$31,406

COLLABORATION_AND_LICENSE_AGRE2

COLLABORATION AND LICENSE AGREEMENTS (Details) (USD $)

12 Months Ended

3 Months Ended

12 Months Ended

127 Months Ended

3 Months Ended

12 Months Ended

3 Months Ended

12 Months Ended

1 Months Ended

3 Months Ended

12 Months Ended

1 Months Ended

12 Months Ended

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2012

Sep. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2012

Jun. 30, 2014

Sep. 30, 2011

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2012

Sep. 30, 2013

Jun. 30, 2014

Jul. 31, 2013

Jun. 30, 2013

Mar. 31, 2011

Dec. 31, 2013

Sep. 30, 2013

Dec. 31, 2012

Jun. 30, 2011

Jun. 30, 2010

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2012

31-May-13

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jul. 31, 2013

Jun. 30, 2014

Jul. 31, 2014

Celgene

Genentech 2003 Collaboration Agreement

Genentech Chk-1 Agreement

Genentech, Inc.

Loxo Oncology, Inc.

Novartis International Pharmaceutical Ltd.

Oncothyreon Inc.

Loxo Oncology, Inc.

Reimbursable Expenses

Subsequent Event

Deliverable

drug

Deliverable

Entity

U.S.

Outside of the U.S.

Oncothyreon Inc.

Loxo Oncology, Inc.

Deliverable

Renewal

Deliverable

Collaboration and License Agreements, by Type [Line Items]

Up-front payment received

$11,000,000

$28,000,000

$10,000,000

Additional aggregate potential nonrefundable milestone payments

376,000,000

24,000,000

380,000,000

435,000,000

408,000,000

Number of non-contingent deliverables related to agreement

Collaborative Arrangement, Estimated Option Term Under Agreement

'3 years

Collaborative Arrangement, Estimated Option Term Under Agreement, Extension Period

'1 year

Collaboration revenue

16,967,000

12,854,000

13,886,000

3,700,000

135,000

2,300,000

8,800,000

5,200,000

3,500,000

2,600,000

Notice period for termination of agreement by collaborator

'6 months

'4 months

'60 days

'6 months

'180 days

Up-front and milestone payments received

23,500,000

5,000,000

10,000,000

45,000,000

Number of partnered drugs

License and milestone revenue

25,111,000

56,726,000

71,249,000

3,400,000

5,300,000

25,900,000

Collaborative Arrangement, Term of Discovery Research Phase

'3 years

Collaborative Arrangement, Number of Agreement Extensions

Collaborative Arrangement, Term of Discovery Research Phase, Renewal Period

'1 year

Cost Method Investment, Ownership Percentage

15.30%

19.90%

10.00%

Estimated fair value of shares

4,500,000

Milestone payment earned

5,000,000

10,000,000

Licenses revenue

4,500,000

8,000,000

10,000,000

Milestone revenue

4,000,000

7,700,000

3,800,000

Notice period for termination in the event of a material breach of a material obligation under the agreement

'90 days

Percentage of reimbursement of development costs by collaborator during the first two years of the co-development period

100.00%

Co-development payment issued to partner

11,300,000

9,200,000

Entity's share of combined development costs

18,900,000

11,800,000

5,600,000

Payable recorded for entity's portion of the development costs

11,000,000

16,200,000

11,000,000

Receivable for reimbursable development costs

$3,700,000

$4,100,000

$3,700,000

Percentage of development costs responsible for

50.00%

Co-promotion right, percentage

50.00%

Percentage share of profit or loss

50.00%

Percentage of profit that royalty on net sales is intended to approximate

50.00%

Number of companies that share equally in proceeds from sublicense marketing rights

COLLABORATION_AND_LICENSE_AGRE3

COLLABORATION AND LICENSE AGREEMENTS (Schedule Of Deferred Revenue) (Details) (USD $)	Jun. 30, 2014	Jun. 30, 2013
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013
Total deferred revenue	$9,546	$14,353
Less: Current portion	-6,193	-14,353
Deferred revenue, long-term portion	3,353	0
Celgene	'	'
Total deferred revenue	7,258	0
Biogen Idec	'	'
Total deferred revenue	1,218	0
Loxo Oncology, Inc.	'	'
Total deferred revenue	625	0
Genentech, Inc.	'	'
Total deferred revenue	367	2,300
Novartis International Pharmaceutical Ltd.	'	'
Total deferred revenue	0	12,053
Other Partners	'	'
Total deferred revenue	$78	$0

LONGTERM_DEBT_Narrative_Detail

LONG-TERM DEBT (Narrative) (Details) (USD $)

12 Months Ended

0 Months Ended

12 Months Ended

0 Months Ended

12 Months Ended

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2012

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Mar. 31, 2014

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 10, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 10, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 10, 2013

Jun. 30, 2014

Comerica Loan and Security Agreement

Convertible Senior Notes, due 2020

Deerfield Credit Facilities

Scenario One

Scenario Two

Line of credit

Senior subordinated notes

Secured debt

Comerica Loan and Security Agreement

Comerica Bank

Term loan

Revolving line of credit

Other noncurrent assets

Additional paid-in capital

Quoted prices for similar assets observable in the marketplace (Level 2)

instrument

Line of credit

Comerica Bank

Term loan

Quoted prices for similar assets observable in the marketplace (Level 2)

Comerica Bank

Prime rate

Debt Instrument [Line Items]

Maximum borrowing capacity

$15,000,000

$6,800,000

Long-term debt, outstanding

146,800,000

14,550,000

132,250,000

Description of variable interest rate basis

'Prime Rate

Balance of cash, cash equivalents and marketable securities maintained at Comerica, if amount is greater than or equal to, interest is Scenario One

10,000,000

Basis spread on variable interest rate (up to)

2.00%

Balance of cash, cash equivalents and marketable securities maintained at Comerica, if amount is less than, interest is Scenario Two

10,000,000

Interest rate at period end (as a percent)

3.25%

22,000,000

Financial ratio required to be maintained under covenant

1.25

Fair value of term loan

14,600,000

Stated interest rate

3.00%

Debt instrument, face amount

132,300,000

Proceeds from debt issuance

128,000,000

Convertible debt, conversion rate

0.1419

Convertible debt, conversion price

$7.05

Percentage of principal amount of convertible debt required to be repurchased upon qualifying change in control or termination of trading of common stock

100.00%

Convertible debt, threshold percentage of stock price trigger

130.00%

Convertible debt, threshold trading days

Convertible debt, threshold consecutive trading days

'30 days

Convertible debt, threshold consecutive trading days, number of days immediately prior to redemption notice date

'7 days

Convertible debt, redemption price, percentage of principal amount to be redeemed

100.00%

Convertible debt, interest rate, effective percentage

10.25%

Convertible debt, liability component

84,200,000

Convertible debt, equity component

48,000,000

Underwriting discount and offering expenses

4,300,000

2,700,000

1,600,000

Unamortized debt issuance costs

2,400,000

Fair value of notes

132,300,000

126,000,000

Number of outstanding credit facilities

Repayment of debt

$92,712,000

$4,350,000

$92,600,000

LONGTERM_DEBT_Schedule_of_Long

LONG-TERM DEBT (Schedule of Long-Term Debt) (Details) (USD $)	Jun. 30, 2014	Jun. 30, 2013
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013
Debt Instrument [Line Items]	'	'
Long-term debt, gross	$146,800	$146,800
Less: Unamortized debt discount	-42,848	-47,779
Long-term debt, net	103,952	99,021
Senior subordinated notes \| Convertible Senior Notes, due 2020	'	'
Debt Instrument [Line Items]	'	'
Long-term debt, gross	132,250	132,250
Term loan \| Line of credit \| Comerica Loan and Security Agreement	'	'
Debt Instrument [Line Items]	'	'
Long-term debt, gross	$14,550	$14,550

LONGTERM_DEBT_Loss_on_Prepayme

LONG-TERM DEBT (Loss on Prepayment of Long-term Debt) (Details) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2012
Debt Instrument [Line Items]	'	'	'
Loss on prepayment of long-term debt, net	$0	($11,197)	($942)
Deerfield Credit Facilities \| Secured debt	'	'	'
Debt Instrument [Line Items]	'	'	'
Write off proportional value or remaining balance of the debt discount	'	-10,898	-887
Write off proportional value or remaining balance of the unamortized debt issuance costs	'	-720	-55
Fair value adjustment for, or write off of, the embedded derivatives	'	421	0
Loss on prepayment of long-term debt, net	'	($11,197)	($942)

LONGTERM_DEBT_Summary_of_Inter

LONG-TERM DEBT (Summary of Interest Expense) (Details) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2012
Debt Instrument [Line Items]	'	'	'
Amortization of debt discounts and transaction fees	$5,258	$4,476	$4,643
Total interest expense	9,716	11,258	11,624
Comerica Loan and Security Agreement \| Term loan	'	'	'
Debt Instrument [Line Items]	'	'	'
Simple interest	479	483	489
Amortization of transaction fees and debt issuance costs	48	107	108
Total interest expense	527	590	597
Convertible Senior Notes, due 2020	'	'	'
Debt Instrument [Line Items]	'	'	'
Simple interest	3,979	221	0
Amortization of transaction fees and debt issuance costs	278	14	0
Amortization of debt discount	4,932	259	0
Total interest expense	9,189	494	0
Deerfield Credit Facilities	'	'	'
Debt Instrument [Line Items]	'	'	'
Simple interest	0	6,078	6,492
Amortization of debt discounts and transaction fees	0	4,331	4,419
Change in fair value of the embedded derivatives	0	-235	116
Total interest expense	$0	$10,174	$11,027

LONGTERM_DEBT_Commitment_Sched

LONG-TERM DEBT (Commitment Schedule) (Details) (USD $)	Jun. 30, 2014	Jun. 30, 2013
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013
Debt Disclosure [Abstract]	'	'
2015	$0	'
2016	0	'
2017	0	'
2018	14,550	'
2019	0	'
Thereafter	132,250	'
Long-term debt, gross	$146,800	$146,800

COMMITMENTS_AND_CONTINGENCIES_1

COMMITMENTS AND CONTINGENCIES (Details) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2012
	Term	Jun. 30, 2013	Jun. 30, 2012
Commitments and Contingencies Disclosure [Abstract]	'	'	'
Option to extend lease, number of terms	2	'	'
Option to extend lease, lease term	'5 years	'	'
Future minimum rental commitments	'	'	'
2015	$8,316	'	'
2016	8,338	'	'
2017	368	'	'
2018	0	'	'
2019	0	'	'
Thereafter	0	'	'
Total minimum rental commitments	17,022	'	'
Rent expense	'	'	'
Cash paid for rent	8,878	8,625	8,549
Deferred rent credits	-3,645	-3,489	-3,332
Rent expense, net	$5,233	$5,136	$5,217

STOCKHOLDERS_DEFICIT_Details

STOCKHOLDERS' DEFICIT (Details) (USD $)	12 Months Ended					12 Months Ended		12 Months Ended
	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2014	Jun. 30, 2014	Jun. 30, 2014	Jun. 30, 2014	Jun. 30, 2014	Mar. 27, 2013
				Warrant Issuance One	Warrant Issuance Two	Stock Option and Incentive Plan	Stock Option and Incentive Plan	Common Stock	Common Stock
							Incentive stock options
Stock Option and Incentive Plan	'	'	'	'	'	'	'	'	'
Shares of common stock reserved for future issuance under the Option and Incentive Plan	'	'	'	'	'	23,131,696	1,690,965	'	'
Additional shares authorized as a percentage of shares issued and outstanding	'	'	'	'	'	25.00%	'	'	'
Vesting period	'	'	'	'	'	'4 years	'	'	'
Expiration term	'	'	'	'	'	'10 years	'	'	'
Warrants	'	'	'	'	'	'	'	'	'
Number of warrants	'	'	'	6,000,000	6,000,000	'	'	'	'
Exercise price of warrants	'	'	'	3.65	4.19	'	'	'	'
Controlled Equity Offering	'	'	'	'	'	'	'	'	'
Dollar amount of stock that may be sold under the agreement	'	'	'	'	'	'	'	'	$75,000,000
Commission under sales agreement	'	'	'	'	'	'	'	'	2.00%
Issuance of stock (in shares)	'	'	'	'	'	'	'	13,800,000	'
Average Share Price	'	'	'	'	'	'	'	$5.43	'
Proceeds from the issuance of common stock	75,000,000	75,555,000	67,145,000	'	'	'	'	75,000,000	'
Commissions	'	'	'	'	'	'	'	$1,500,000	'

SHAREBASED_COMPENSATION_Narrat

SHARE-BASED COMPENSATION (Narrative) (Details) (USD $)	12 Months Ended
SHARE-BASED COMPENSATION (Narrative) (Details) (USD $)	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2012
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'
Share-based compensation expense	$4,300,000	$3,400,000	$2,400,000
Stock Option and Incentive Plan	'	'	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'
Closing stock price (in dollars per share)	$4.56	'	'
Total intrinsic value of all options exercised	2,000,000	853,000	78,000
Total unrecognized compensation expense	$8,600,000	'	'
Weighted-average period for recognition of unrecognized compensation expense (in years)	'3 years	'	'
Shares of common stock reserved for issuance under the ESPP	23,131,696	'	'
Employee Stock Purchase Plan	'	'	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'
Shares of common stock reserved for issuance under the ESPP	4,650,000	'	'
Purchase price of common stock (as a percent)	85.00%	'	'
Original offering period (in months)	'12 months	'	'
New offering period on termination of original offering period (in months)	'6 months	'	'
Common shares available for issuance under ESPP (in shares)	491,649	'	'
Shares issued under ESPP (in shares)	309,287	524,296	443,651

SHAREBASED_COMPENSATION_Detail

SHARE-BASED COMPENSATION (Details) (USD $)	12 Months Ended
In Thousands, except Share data, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2012
Fair Value Assumptions	'	'	'
Risk-free interest rate, minimum	1.70%	0.80%	0.90%
Risk-free interest rate, maximum	2.10%	1.20%	1.50%
Expected option term in years	'6 years 3 months	'6 years 3 months	'6 years 3 months
Expected volatility, minimum (as a percent)	67.80%	66.00%	63.80%
Expected volatility, maximum (as a percent)	68.90%	67.50%	65.80%
Dividend yield (as a percent)	0.00%	0.00%	0.00%
Weighted average grant date fair value (in dollars per share)	$2.91	$3.07	$2.04
Number of Options [Roll Forward]	'	'	'
Number of Options Outstanding, beginning of period	10,337,737	'	'
Number of Options, Granted	2,454,244	'	'
Number of Options, Exercised	-859,472	'	'
Number of Options, Forfeited	-1,675,631	'	'
Number of Options, Expired or canceled	-62,061	'	'
Number of Options Outstanding, end of period	10,194,817	10,337,737	'
Number of Options, Vested and expected to vest at end of period	8,491,883	'	'
Number of Options, Exercisable at end of period	4,712,643	'	'
Weighted Average Exercise Price [Roll Forward]	'	'	'
Weighted Average Exercise Price, beginning of period	$4.87	'	'
Weighted Average Exercise Price, Granted	$4.63	'	'
Weighted Average Exercise Price, Exercised	$3.33	'	'
Weighted Average Exercise Price, Forfeited	$5.43	'	'
Weighted Average Exercise Price, Expired or Canceled	$8.23	'	'
Weighted Average Exercise Price, end of period	$4.84	$4.87	'
Weighted Average Exercise Price, Vested and expected to vest at end of period	$4.91	'	'
Weighted Average Exercise Price, Exercisable at end of period	$5.27	'	'
Weighted Average Remaining Contractual Term, Number of Options Outstanding, end of period (in years)	'7 years 0 months	'	'
Weighted Average Remaining Contractual Term, Vested and expected to vest at end of period (in years)	'6 years 8 months	'	'
Weighted Average Remaining Contractual Term, Exercisable at end of period (in years)	'4 years 11 months	'	'
Aggregate Intrinsic Value, Number of Options Outstanding, end of period	$4,656	'	'
Aggregate Intrinsic Value, Vested and expected to vest at end of period	4,182	'	'
Aggregate Intrinsic Value, Exercisable at end of period	$2,931	'	'

EMPLOYEE_BENEFIT_PLAN_Details

EMPLOYEE BENEFIT PLAN (Details) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2012
Compensation and Retirement Disclosure [Abstract]	'	'	'
Minimum percentage of salary that participants can contribute under the 401(k) plan	1.00%	'	'
Maximum percentage of salary that participants can contribute under the 401(k) plan	60.00%	'	'
Employer matching contribution, percent of employee contributions	4.00%	'	'
Matching contributions by company	$1,200	$820	$1,000

RESTRUCTURING_CHARGES_Details

RESTRUCTURING CHARGES (Details) (Fiscal 2014 Restructuring, Reduction in workforce, USD $)	0 Months Ended	3 Months Ended
In Thousands, unless otherwise specified	Aug. 05, 2013	Dec. 31, 2013	Sep. 30, 2013
Restructuring Cost and Reserve [Line Items]	'	'	'
Restructuring and Related Cost, Number of Positions Eliminated, Period Percent	20.00%	'	'
Restructuring charge	'	'	$2,800
Payment for restructuring expense	'	194	2,600
Research and Development for Proprietary Drug Discovery	'	'	'
Restructuring Cost and Reserve [Line Items]	'	'	'
Restructuring charge	'	'	2,200
General and Administrative Expenses	'	'	'
Restructuring Cost and Reserve [Line Items]	'	'	'
Restructuring charge	'	'	$602

INCOME_TAXES_Schedule_of_Recon

INCOME TAXES (Schedule of Reconciliation of Income Taxes at the Statutory Federal Income Tax Rate to Net Income Taxes) (Details)	12 Months Ended
	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2012
Income Tax Disclosure [Abstract]	'	'	'
U.S. federal income tax expense at the statutory rate	34.00%	34.00%	34.00%
Interest expense disallowed under Sec.163(l)	0.00%	-5.00%	-15.60%
Available research and experimentation tax credits	2.00%	5.70%	12.90%
Stock-based compensation	-1.20%	-3.80%	-2.60%
(Gain)/loss on early prepayment of debt	0.00%	-6.10%	-1.40%
FIN 48 reserve releases	-0.30%	-0.70%	7.30%
Rate change	0.00%	-0.80%	-2.20%
Effect of other permanent differences	-0.10%	0.20%	0.00%
State income taxes, net of federal taxes	3.10%	2.00%	1.40%
Valuation allowance	-37.50%	-25.50%	-33.80%
Total	0.00%	0.00%	0.00%

INCOME_TAXES_Schedule_of_Defer

INCOME TAXES (Schedule of Deferred Tax Assets and Liabilities) (Details) (USD $)	Jun. 30, 2014	Jun. 30, 2013
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013
Current deferred tax assets, gross	'	'
Accrued benefits	$2,402	$2,725
Inventory reserve	1,514	1,203
Total current deferred tax assets	3,916	3,928
Non-current deferred tax assets, gross	'	'
Net operating loss carryforwards	196,997	162,791
Capital loss carryforwards	6,095	6,094
Research and experimentation credit carryforwards	28,558	27,060
Deferred revenue	197	4,951
Deferred rent	2,909	4,261
Depreciation of property and equipment	7,666	6,885
Loan costs on convertible senior notes	469	565
Other	2,333	2,439
Total non-current deferred tax assets	245,224	215,046
Total deferred tax assets	249,140	218,974
Long-term deferred tax liability	'	'
Discount on convertible senior notes	15,905	17,734
Total long-term deferred tax liability	15,905	17,734
Deferred tax assets, net of deferred tax liability	233,235	201,240
Valuation allowance	-233,235	-201,240
Deferred tax assets, net of valuation allowance	$0	$0

INCOME_TAXES_Unrecognized_Tax_

INCOME TAXES (Unrecognized Tax Benefits) (Details) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013
Unrecognized tax benefits	'	'
Balance at beginning of year	$3,428	$2,968
Additions based on tax positions related to the current year	712	915
Additions for tax positions of prior year	0	-2
Reductions for tax positions of prior year	-464	-453
Balance at end of year	$3,676	$3,428

INCOME_TAXES_INCOME_TAXES_Narr

INCOME TAXES INCOME TAXES (Narrative) (Details) (USD $)	12 Months Ended
INCOME TAXES INCOME TAXES (Narrative) (Details) (USD $)	Jun. 30, 2014	Jun. 30, 2013
Tax Credit Carryforward [Line Items]	'	'
Unrealized excess tax benefits from stock option exercises, before valuation allowance	$4,600,000	$4,500,000
Net operating loss carryforwards	545,300,000	'
Net operating losses limited in ability to offset taxable income	40,000	'
Federal \| Research and experimentation	'	'
Tax Credit Carryforward [Line Items]	'	'
Tax credit carryforwards	$31,500,000	'

SELECTED_QUARTERLY_FINANCIAL_D2

SELECTED QUARTERLY FINANCIAL DATA (UNAUDITED) (Details) (USD $)	3 Months Ended								12 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Jun. 30, 2014	Mar. 31, 2014	Dec. 31, 2013	Sep. 30, 2013	Jun. 30, 2013	Mar. 31, 2013	Dec. 31, 2012	Sep. 30, 2012	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2012
Quarterly Financial Information Disclosure [Abstract]	'	'	'	'	'	'	'	'	'	'	'
Revenue	$6,011	$7,773	$14,066	$14,228	$25,415	$9,955	$18,377	$15,833	$42,078	$69,580	$85,135
Research and development for proprietary programs	14,502	14,131	9,487	11,704	16,840	15,105	13,941	13,534	49,824	59,420	56,719
Total operating expenses	31,794	30,292	28,069	27,541	29,079	28,730	26,460	24,853	117,696	109,122	96,182
Net loss	($28,237)	($24,932)	($16,408)	($15,680)	($17,649)	($21,594)	($10,931)	($11,768)	($85,257)	($61,942)	($23,581)
Weighted average shares outstanding b basic and diluted	126,815	125,471	123,921	117,509	116,792	116,665	105,403	92,606	123,403	107,794	70,619
Net loss per share b basic and diluted	($0.22)	($0.20)	($0.13)	($0.13)	($0.15)	($0.19)	($0.10)	($0.13)	($0.69)	($0.57)	($0.33)

SUBSEQUENT_EVENT_Details

SUBSEQUENT EVENT (Details) (Subsequent Event, USD $)	Jul. 31, 2014
In Millions, except Per Share data, unless otherwise specified	Jul. 31, 2014
Subsequent Event [Line Items]	'
Common Stock Sold By Third Party, Price Per Share	$13
Loxo Oncology, Inc.	'
Subsequent Event [Line Items]	'
Available-for-sale Securities, Number of Shares	1.6
Cost Method Investment, Ownership Percentage	10.00%