License Agreements	12 Months Ended
Dec. 31, 2011
License Agreements [Abstract]
License Agreements	10. License Agreements *Collaboration Agreement—Astellas* In June 2009, NeurogesX entered into the Astellas Agreement granting Astellas an exclusive license to commercialize Qutenza in the Licensed Territory. The Astellas Agreement provided for an upfront payment for past development and the commercialization rights granted, of 30 million Euro, or $41.8 million. In addition, the agreement provided for an upfront payment of 5 million Euro, or $7.0 million, for future development expenses and an option to license NGX-1998, a product candidate in Phase 1 development at that time. Other elements of the Astellas Agreement include future payments of up to 65 million Euro if certain pre-defined sales thresholds of the products licensed under the agreement are met and royalties, as a percentage of net sales made by Astellas of products under the agreement, with such royalties starting in the high teens and escalating into the mid twenties as revenues increase. The Company is participating on a joint steering committee with Astellas to oversee the development and commercialization activities related to Qutenza and NGX-1998 during the term of the agreement, not to exceed ten years. On the seventh anniversary of the Astellas Agreement, the Company has the unilateral right to opt-out of participation on the joint steering committee. The Astellas Agreement further provides that upon delivery of certain data related to NGX-1998, Astellas may pay two additional NGX-1998 option payments totaling 5 million Euro. Subsequent to Astellas' exercise of the option to exclusively license NGX-1998 in the Territory, both companies would cooperate on Phase III clinical trials and will share such costs equally. The Company commenced recognizing revenue related to the upfront and option payments upon transfer of the Marketing Authorization for Qutenza to Astellas, which occurred in September 2009. For the years ended December 31, 2011, 2010 and 2009, the Company recognized $7.2 million, $7.2 million and $1.9 million as Collaboration revenue related to the upfront and option payments, respectively. As of December 31, 2011, the Company had deferred revenue totaling $32.4 million, of which $7.3 million is reflected as current. The Astellas upfront license fee and option payments are accounted for as a single unit of accounting, and accordingly, such payments will be recognized ratably through June 2016, which is the Company's estimate of its substantive performance obligation period related to the joint steering committee. Subsequent option exercise payments received, if any, are expected to be recognized ratably over the remaining estimated period of performance. The agreement will remain effective on a country-by-country and product-by-product basis until the later of ten years after the first commercial sale, expiration or abandonment of the last valid patent claim or expiration of all applicable periods of regulatory exclusivity. Astellas may terminate the agreement for any reason without penalty, consequence or compensation on a country-by-country and product-by-product basis upon written notice to the Company. Pursuant to the Supply Agreement, the Company has agreed to provide Astellas with a sufficient supply of Qutenza to support their commercialization efforts until Astellas can establish a direct supply relationship with product vendors. These products will be charged to Astellas at contractually agreed upon costs per unit which are intended to reflect the Company's direct cost of goods and related internal labor and overhead costs without mark-up for profit. The Company reported amounts received from product transactions net of direct costs incurred as a component of Collaboration revenue. For the years ended December 31, 2011, 2010 and 2009, the Company included in Collaboration revenue $0.8 million, $0.3 million and $0.1 million from product transactions, net of direct costs incurred as a component of Collaboration revenue, respectively. For the years ended December 31, 2011 and 2010, the Company recognized $0.9 million and a nominal amount, respectively, in royalty revenue related to the Astellas Agreement as a component of Collaboration revenue. There was no royalty revenue in 2009. *University Of California* In October 2000 and as amended, the Company licensed certain patents, including a method patent, from the University of California ("UC") for prescription strength capsaicin for neuropathic pain. Under the terms of the agreement, the Company is required to pay royalties on net sales of the licensed product up to a maximum of $1.0 million per annum, as well as a percentage of upfront and milestone payments received by the Company from sublicensing the Company's rights under the agreement ("Sublicense Fee"). As a result of the Astellas license payment received in July 2009, the Company accrued a $1.2 million sublicense fee to research and development expense during the third quarter of 2009, which was paid in February 2010. The Company recognized $14,000 and $4,000, respectively, in royalty expense due to UC for the years ended December 31, 2011 and 2010 related to Qutenza product sales in the United States. Two of the three inventors named in the method patent did not assign their patent rights to UC. These non-assigning inventors have made various claims related to inventorship and other matters. In 2010, the Company entered into negotiations with these non-assigning inventors to settle any and all claims and to have them assign their rights related to the method patent and any other related patent rights that may exist at the time we enter into a final binding settlement agreement. The Company anticipates that a final settlement may include the Company issuing stock or stock options to the two non-assigning inventors and making current and future cash payments. The Company anticipates that approximately 50% of the cash settlement amount will be recovered over time, through a reduction in amounts due to the University of California under the Company's license agreement with them. During the year ended December 31, 2010, the Company recorded a $1.0 million charge within selling, general and administrative expense representing its estimate of the potential settlement. In 2011, the Company continued negotiations and has revised its estimate of the potential settlement down to $0.7 million, which is the current cash and estimated fair value of the stock or stock options to be issued as part of a potential settlement. The estimated amount to be paid is included in Other accrued expenses on the consolidated balance sheets. *LTS Lohmann Therapie-Systeme AG* In January 2007, the Company entered into a Commercial Supply and License Agreement ("LTS Agreement") with LTS Lohmann Therapie-Systeme AG ("LTS") to manufacture commercial and clinical supply of Qutenza. Under the terms of the agreement, the Company is required to pay a transfer price for product purchased, as well as a royalty on net sales of product purchased under the LTS Agreement. In addition, upon first market approval of Qutenza, the Company is required to make a one-time milestone payment of 100,000 Euros. During the second quarter of 2009, the Company received market approval of Qutenza in the European Union and as a result, paid LTS a one-time milestone payment of 100,000 Euros, or approximately $140,000, which was charged to research and development expense. The Company recognized $47,000 and $12,000, respectively, in royalty expense due to LTS Lohmann Therapie-Systeme AG for the years ended December 31, 2011 and 2010 related to Qutenza product sales in the United States. The Company's December 31, 2011 consolidated balance sheet includes a liability for royalties due UC and LTS totaling $21,000 related to gross product shipments in the year ended December 31, 2011.

10. License Agreements

Collaboration Agreement—Astellas

In June 2009, NeurogesX entered into the Astellas Agreement granting Astellas an exclusive license to commercialize Qutenza in the Licensed Territory. The Astellas Agreement provided for an upfront payment for past development and the commercialization rights granted, of 30 million Euro, or $41.8 million. In addition, the agreement provided for an upfront payment of 5 million Euro, or $7.0 million, for future development expenses and an option to license NGX-1998, a product candidate in Phase 1 development at that time. Other elements of the Astellas Agreement include future payments of up to 65 million Euro if certain pre-defined sales thresholds of the products licensed under the agreement are met and royalties, as a percentage of net sales made by Astellas of products under the agreement, with such royalties starting in the high teens and escalating into the mid twenties as revenues increase. The Company is participating on a joint steering committee with Astellas to oversee the development and commercialization activities related to Qutenza and NGX-1998 during the term of the agreement, not to exceed ten years. On the seventh anniversary of the Astellas Agreement, the Company has the unilateral right to opt-out of participation on the joint steering committee. The Astellas Agreement further provides that upon delivery of certain data related to NGX-1998, Astellas may pay two additional NGX-1998 option payments totaling 5 million Euro. Subsequent to Astellas' exercise of the option to exclusively license NGX-1998 in the Territory, both companies would cooperate on Phase III clinical trials and will share such costs equally.

The Company commenced recognizing revenue related to the upfront and option payments upon transfer of the Marketing Authorization for Qutenza to Astellas, which occurred in September 2009. For the years ended December 31, 2011, 2010 and 2009, the Company recognized $7.2 million, $7.2 million and $1.9 million as Collaboration revenue related to the upfront and option payments, respectively. As of December 31, 2011, the Company had deferred revenue totaling $32.4 million, of which $7.3 million is reflected as current. The Astellas upfront license fee and option payments are accounted for as a single unit of accounting, and accordingly, such payments will be recognized ratably through June 2016, which is the Company's estimate of its substantive performance obligation period related to the joint steering committee. Subsequent option exercise payments received, if any, are expected to be recognized ratably over the remaining estimated period of performance.

The agreement will remain effective on a country-by-country and product-by-product basis until the later of ten years after the first commercial sale, expiration or abandonment of the last valid patent claim or expiration of all applicable periods of regulatory exclusivity. Astellas may terminate the agreement for any reason without penalty, consequence or compensation on a country-by-country and product-by-product basis upon written notice to the Company.

Pursuant to the Supply Agreement, the Company has agreed to provide Astellas with a sufficient supply of Qutenza to support their commercialization efforts until Astellas can establish a direct supply relationship with product vendors. These products will be charged to Astellas at contractually agreed upon costs per unit which are intended to reflect the Company's direct cost of goods and related internal labor and overhead costs without mark-up for profit. The Company reported amounts received from product transactions net of direct costs incurred as a component of Collaboration revenue.

For the years ended December 31, 2011, 2010 and 2009, the Company included in Collaboration revenue $0.8 million, $0.3 million and $0.1 million from product transactions, net of direct costs incurred as a component of Collaboration revenue, respectively.

For the years ended December 31, 2011 and 2010, the Company recognized $0.9 million and a nominal amount, respectively, in royalty revenue related to the Astellas Agreement as a component of Collaboration revenue. There was no royalty revenue in 2009.

University Of California

In October 2000 and as amended, the Company licensed certain patents, including a method patent, from the University of California ("UC") for prescription strength capsaicin for neuropathic pain. Under the terms of the agreement, the Company is required to pay royalties on net sales of the licensed product up to a maximum of $1.0 million per annum, as well as a percentage of upfront and milestone payments received by the Company from sublicensing the Company's rights under the agreement ("Sublicense Fee"). As a result of the Astellas license payment received in July 2009, the Company accrued a $1.2 million sublicense fee to research and development expense during the third quarter of 2009, which was paid in February 2010. The Company recognized $14,000 and $4,000, respectively, in royalty expense due to UC for the years ended December 31, 2011 and 2010 related to Qutenza product sales in the United States.

Two of the three inventors named in the method patent did not assign their patent rights to UC. These non-assigning inventors have made various claims related to inventorship and other matters. In 2010, the Company entered into negotiations with these non-assigning inventors to settle any and all claims and to have them assign their rights related to the method patent and any other related patent rights that may exist at the time we enter into a final binding settlement agreement. The Company anticipates that a final settlement may include the Company issuing stock or stock options to the two non-assigning inventors and making current and future cash payments. The Company anticipates that approximately 50% of the cash settlement amount will be recovered over time, through a reduction in amounts due to the University of California under the Company's license agreement with them. During the year ended December 31, 2010, the Company recorded a $1.0 million charge within selling, general and administrative expense representing its estimate of the potential settlement. In 2011, the Company continued negotiations and has revised its estimate of the potential settlement down to $0.7 million, which is the current cash and estimated fair value of the stock or stock options to be issued as part of a potential settlement. The estimated amount to be paid is included in Other accrued expenses on the consolidated balance sheets.

LTS Lohmann Therapie-Systeme AG

In January 2007, the Company entered into a Commercial Supply and License Agreement ("LTS Agreement") with LTS Lohmann Therapie-Systeme AG ("LTS") to manufacture commercial and clinical supply of Qutenza. Under the terms of the agreement, the Company is required to pay a transfer price for product purchased, as well as a royalty on net sales of product purchased under the LTS Agreement. In addition, upon first market approval of Qutenza, the Company is required to make a one-time milestone payment of 100,000 Euros. During the second quarter of 2009, the Company received market approval of Qutenza in the European Union and as a result, paid LTS a one-time milestone payment of 100,000 Euros, or approximately $140,000, which was charged to research and development expense. The Company recognized $47,000 and $12,000, respectively, in royalty expense due to LTS Lohmann Therapie-Systeme AG for the years ended December 31, 2011 and 2010 related to Qutenza product sales in the United States.

The Company's December 31, 2011 consolidated balance sheet includes a liability for royalties due UC and LTS totaling $21,000 related to gross product shipments in the year ended December 31, 2011.