10-Q

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 10-Q

(Mark One)

R QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the Quarterly Period Ended March 31, 2013

or

q TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the Transition Period from _____________ to _____________

Commission File Number:  000-30111

Lexicon Pharmaceuticals, Inc.

(Exact Name of Registrant as Specified in its Charter)

Delaware	76-0474169
(State or Other Jurisdiction of Incorporation or Organization)	(I.R.S. Employer Identification Number)

8800 Technology Forest Place

The Woodlands, Texas 77381

(Address of Principal Executive Offices and Zip Code)

(281) 863-3000

(Registrant’s Telephone Number, Including Area Code)

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports) and (2) has been subject to such filing requirements for the past 90 days.

Yes þ No

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files).

Yes þ No

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company.  See the definitions of “large accelerated filer,” “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act.

Large accelerated filer    Accelerated filer þ Non-accelerated filer    Smaller reporting company

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act).

Yes No þ

As of May 6, 2013, 513,025,272 shares of the registrant’s common stock, par value $0.001 per share, were outstanding.

Lexicon Pharmaceuticals, Inc.

Table of Contents

		Page
Factors Affecting Forward-Looking Statements		2
Part I – Financial Information		3
Item 1.	Financial Statements	3
	Consolidated Balance Sheets – March 31, 2013 (unaudited) and December 31, 2012	3
	Consolidated Statements of Comprehensive Loss (unaudited) – Three Months Ended March 31, 2013 and 2012	4
	Consolidated Statements of Stockholders’ Equity (unaudited) – Three Months Ended March 31, 2013 and 2012	5
	Consolidated Statements of Cash Flows (unaudited) – Three Months Ended March 31, 2013 and 2012	6
	Notes to Consolidated Financial Statements (unaudited)	7
Item 2.	Management’s Discussion and Analysis of Financial Condition and Results of Operations	13
Item 3.	Quantitative and Qualitative Disclosures About Market Risk	18
Item 4.	Controls and Procedures	18
Part II – Other Information		19
Item 1.	Legal Proceedings	19
Item 1A.	Risk Factors	19
Item 2.	Unregistered Sales of Equity Securities and Use of Proceeds	21
Item 6.	Exhibits	21
Signatures		22

The Lexicon name and logo, OmniBank^® and LexVision^® are registered trademarks and Genome5000^™ is a trademark of Lexicon Pharmaceuticals, Inc.

——————

Factors Affecting Forward Looking Statements

This quarterly report on Form 10-Q contains forward-looking statements. These statements relate to future events or our future financial performance. We have attempted to identify forward-looking statements by terminology including “anticipate,” “believe,” “can,” “continue,” “could,” “estimate,” “expect,” “intend,” “may,” “plan,” “potential,” “predict,” “should” or “will” or the negative of these terms or other comparable terminology. These statements are only predictions and involve known and unknown risks, uncertainties and other factors, including the risks outlined under “Part II, Item 1A. - Risk Factors,” that may cause our or our industry's actual results, levels of activity, performance or achievements to be materially different from any future results, levels or activity, performance or achievements expressed or implied by these forward-looking statements.

Although we believe that the expectations reflected in the forward-looking statements are reasonable, we cannot guarantee future results, levels of activity, performance or achievements. We are not under any duty to update any of the forward-looking statements after the date of this quarterly report on Form 10-Q to conform these statements to actual results, unless required by law.

2

Part I – Financial Information

Item 1.                 Financial Statements

Lexicon Pharmaceuticals, Inc.

Consolidated Balance Sheets

(In thousands, except par value)

	As of March 31,			As of December 31,
	2013			2012
Assets	(unaudited)
Current assets:
Cash and cash equivalents	$	34,248		$	30,423
Short-term investments, including restricted investments of $430	162,915			192,785
Accounts receivable, net of allowances of $35	863			1,378
Prepaid expenses and other current assets	8,438			6,349
Total current assets	206,464			230,935
Property and equipment, net of accumulated depreciation and amortization of $80,882 and $83,416, respectively	42,623			42,634
Goodwill	44,543			44,543
Other intangible assets	53,557			53,557
Other assets	88			109
Total assets	$	347,275		$	371,778
Liabilities and Equity
Current liabilities:
Accounts payable	$	5,442		$	7,661
Accrued liabilities	9,704			8,922
Current portion of deferred revenue	628			128
Current portion of long-term debt	1,607			1,574
Total current liabilities	17,381			18,285
Deferred revenue, net of current portion	13,405			13,910
Long-term debt	21,457			21,877
Deferred tax liabilities	18,745			18,745
Other long-term liabilities	34,079			32,283
Total liabilities	105,067			105,100
Commitments and contingencies
Equity:
Preferred stock, $.01 par value; 5,000 shares authorized; no shares issued and outstanding	—			—
Common stock, $.001 par value; 900,000 shares authorized; 513,835 and 512,375 shares issued, respectively	514			512
Additional paid-in capital	1,168,961			1,166,605
Accumulated deficit	(925,806		)	(899,832		)
Accumulated other comprehensive gain	42			23
Treasury stock, at cost, 814 and 380 shares, respectively	(1,503		)	(630		)
Total equity	242,208			266,678
Total liabilities and equity	$	347,275		$	371,778

The accompanying notes are an integral part of these consolidated financial statements.

3

Lexicon Pharmaceuticals, Inc.

Consolidated Statements of Comprehensive Loss

(In thousands, except per share amounts)

(Unaudited)

	Three Months Ended March 31,
	2013			2012
Revenues:
Collaborative research	$	284		$	152
Subscription and license fees	76			148
Total revenues	360			300
Operating expenses:
Research and development, including stock-based compensation of $1,330 and $1,037, respectively	20,327			23,037
Increase in fair value of Symphony Icon, Inc. purchase liability	1,264			2,081
General and administrative, including stock-based compensation of $779 and $681, respectively	4,324			4,565
Total operating expenses	25,915			29,683
Loss from operations	(25,555		)	(29,383		)
Interest income	53			56
Interest expense	(506		)	(537		)
Other income (expense), net	34			(4		)
Consolidated net loss	$	(25,974	)	$	(29,868	)
Consolidated net loss per common share, basic and diluted	$	(0.05	)	$	(0.06	)
Shares used in computing consolidated net loss per common share, basic and diluted	512,428			480,324
Other comprehensive loss:
Unrealized gain (loss) on investments	19			(78		)
Comprehensive loss	$	(25,955	)	$	(29,946	)

The accompanying notes are an integral part of these consolidated financial statements.

4

Lexicon Pharmaceuticals, Inc.

Consolidated Statements of Stockholders’ Equity

(In thousands)

(Unaudited)

	Common Stock			Additional						Accumulated Other
	Shares	Par Value		Paid-In Capital			Accumulated Deficit			Comprehensive Gain (Loss)			Treasury Stock			Total
Balance at December 31, 2011	480,389	$	480	$	1,087,033		$	(789,621	)	$	21		$	(345	)	$	297,568
Stock-based compensation	—	—		1,718			—			—			—			1,718
Issuance of common stock under Equity Incentive Plans	553	1		51			—			—			—			52
Other	—	—		(136		)	—			—			—			(136		)
Repurchase of common stock	—	—		—			—			—			(285		)	(285		)
Net loss	—	—		—			(29,868		)	—			—			(29,868		)
Unrealized loss on investments	—	—		—			—			(78		)	—			(78		)
Balance at March 31, 2012	480,942	$	481	$	1,088,666		$	(819,489	)	$	(57	)	$	(630	)	$	268,971
Balance at December 31, 2012	512,375	$	512	$	1,166,605		$	(899,832	)	$	23		$	(630	)	$	266,678
Stock-based compensation	—	—		2,109			—			—			—			2,109
Issuance of common stock under Equity Incentive Plans	1,460	2		247			—			—			—			249
Repurchase of common stock	—	—		—			—			—			(873		)	(873		)
Net loss	—	—		—			(25,974		)	—			—			(25,974		)
Unrealized gain on investments	—	—		—			—			19			—			19
Balance at March 31, 2013	513,835	$	514	$	1,168,961		$	(925,806	)	$	42		$	(1,503	)	$	242,208

The accompanying notes are an integral part of these consolidated financial statements.

5

Lexicon Pharmaceuticals, Inc.

Consolidated Statements of Cash Flows

(In thousands)

(Unaudited)

	Three Months Ended March 31,
	2013			2012
Cash flows from operating activities:
Consolidated net loss	$	(25,974	)	$	(29,868	)
Adjustments to reconcile consolidated net loss to net cash used in operating activities:
Depreciation	793			1,125
Increase in fair value of Symphony Icon, Inc. purchase liability	1,264			2,081
Stock-based compensation	2,109			1,718
Changes in operating assets and liabilities:
Decrease in accounts receivable	515			164
Increase in prepaid expenses and other current assets	(2,089		)	(1,395		)
Decrease in other assets	21			24
Decrease in accounts payable and other liabilities	(905		)	(851		)
Decrease in deferred revenue	(5		)	—
Net cash used in operating activities	(24,271		)	(27,002		)
Cash flows from investing activities:
Purchases of property and equipment	(839		)	(234		)
Proceeds from disposal of property and equipment	57			—
Purchases of investments	(80,954		)	(151,776		)
Maturities of investments	110,843			22,435
Net cash provided by (used in) investing activities	29,107			(129,575		)
Cash flows from financing activities:
Proceeds from issuance of common stock	249			52
Repurchase of common stock	(873		)	(285		)
Repayment of debt borrowings	(387		)	(353		)
Other financing activities	—			(136		)
Net cash used in financing activities	(1,011		)	(722		)
Net increase (decrease) in cash and cash equivalents	3,825			(157,299		)
Cash and cash equivalents at beginning of period	30,423			186,309
Cash and cash equivalents at end of period	$	34,248		$	29,010
Supplemental disclosure of cash flow information:
Cash paid for interest	$	480		$	516
Supplemental disclosure of non-cash investing and financing activities:
Unrealized gain (loss) on investments	$	19		$	(78	)

The accompanying notes are an integral part of these consolidated financial statements.

6

Lexicon Pharmaceuticals, Inc.

Notes to Consolidated Financial Statements

(Unaudited)

1.      Basis of Presentation

The accompanying unaudited consolidated financial statements of Lexicon Pharmaceuticals, Inc. (“Lexicon” or the “Company”) have been prepared in accordance with generally accepted accounting principles for interim financial information and pursuant to the rules and regulations of the Securities and Exchange Commission (“SEC”). Accordingly, they do not include all of the information and footnotes required by generally accepted accounting principles for complete financial statements.

In the opinion of management, all adjustments (consisting of normal recurring adjustments) considered necessary for a fair presentation have been included. Operating results for the three-month period ended March 31, 2013 are not necessarily indicative of the results that may be expected for the year ended December 31, 2013.

The accompanying consolidated financial statements include the accounts of Lexicon and its wholly-owned subsidiaries. Intercompany transactions and balances are eliminated in consolidation.

For further information, refer to the financial statements and footnotes thereto included in Lexicon’s annual report on Form 10-K for the year ended December 31, 2012, as filed with the SEC.

2.      Net Loss Per Share

Net loss per share is computed using the weighted average number of shares of common stock outstanding during the applicable period and excludes shares underlying stock options and restricted stock units because they are antidilutive.  There are no differences between basic and diluted net loss per share for all periods presented.

3.      Stock-Based Compensation

The Company recorded $2.1 million and $1.7 million of stock-based compensation expense for the three months ended March 31, 2013 and 2012, respectively.  The Company utilized the Black-Scholes valuation model for estimating the fair value of the stock compensation granted, with the following weighted-average assumptions for options granted in the three months ended March 31, 2013 and 2012:

	Expected Volatility		Risk-free Interest Rate		Expected Term	Dividend Rate
March 31, 2013:
Employees	91	%	0.8	%	5	—	%
Officers and non-employee directors	81	%	1.6	%	8	—	%
March 31, 2012:
Employees	92	%	0.8	%	5	—	%
Officers and non-employee directors	80	%	1.6	%	8	—	%

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The following is a summary of option activity under Lexicon’s stock-based compensation for the three months ended March 31, 2013:

	Options		Weighted Average Exercise Price
	(in thousands)
Outstanding at December 31, 2012	21,525		$	2.51
Granted	2,971		2.11
Exercised	(140	)	1.78
Expired	(695	)	3.62
Forfeited	(5	)	1.94
Outstanding at March 31, 2013	23,656		2.43
Exercisable at March 31, 2013	16,128		$	2.66

During the three months ended March 31, 2013, Lexicon also granted its employees annual restricted stock units. These restricted stock units vest in four annual installments. The following is a summary of restricted stock units activity under Lexicon’s stock-based compensation plans for the three months ended March 31, 2013:

	Shares		Weighted Average Grant Date Fair Value
	(in thousands)
Outstanding at December 31, 2012	3,543		$	1.80
Granted	1,969		2.09
Vested	(991	)	1.80
Forfeited	(37	)	1.85
Nonvested at March 31, 2013	4,484		$	1.93

During 2010, Lexicon granted certain employees restricted stock units with a performance condition. The shares subject to the restricted stock units granted in 2010 vested upon the dosing of the first patient in a pivotal human clinical trial in any country, the results of which could be used to establish safety and efficacy of a pharmaceutical product discovered or developed by Lexicon as a basis for a New Drug Application. This performance condition occurred during the three months ended March 31, 2013, and therefore all outstanding restricted stock units with this performance condition vested. Stock-based compensation expense for awards with performance conditions is recognized over the period from the date the performance condition is determined to be probable of occurring through the time the applicable condition is met. The following is a summary of performance-based restricted stock units activity under Lexicon's stock-based compensation plans for the three months ended March 31, 2013:

	Shares		Weighted Average Grant Date Fair Value
	(in thousands)
Outstanding at December 31, 2012	329		$	1.90
Vested	(329	)	1.90
Nonvested at March 31, 2013	—		$	—

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4.      Cash and Cash Equivalents and Investments

The fair value of cash and cash equivalents and investments held at March 31, 2013 and December 31, 2012 are as follows:

	As of March 31, 2013
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value
	(in thousands)
Cash and cash equivalents	$	34,248	$	—	$	—		$	34,248
Securities maturing within one year:
Certificates of deposit	550		—		—			550
U.S. treasury securities	162,323		42		—			162,365
Total short-term investments	$	162,873	$	42	$	—		$	162,915
Total cash and cash equivalents and investments	$	197,121	$	42	$	—		$	197,163
	As of December 31, 2012
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value
			(in thousands)
Cash and cash equivalents	$	30,423	$	—	$	—		$	30,423
Securities maturing within one year:
Certificates of deposit	551		—		—			551
U.S. treasury securities	192,211		24		(1		)	192,234
Total short-term investments	$	192,762	$	24	$	(1	)	$	192,785
Total cash and cash equivalents and investments	$	223,185	$	24	$	(1	)	$	223,208

There were no realized gains or losses for the three months ended March 31, 2013, and no realized gains or losses for the three months ended March 31, 2012. The cost of securities sold is based on the specific identification method.

5.      Fair Value Measurements

The Company uses various inputs in determining the fair value of its investments and measures these assets on a recurring basis. Assets and liabilities recorded at fair value in the consolidated balance sheets are categorized by the level of objectivity associated with the inputs used to measure their fair value. The following levels are directly related to the amount of subjectivity associated with the inputs to fair valuation of these assets and liabilities:

• Level 1 - quoted prices in active markets for identical investments

• Level 2 - other significant observable inputs (including quoted prices for similar investments, market corroborated inputs, etc.)

• Level 3 - significant unobservable inputs (including the Company's own assumptions in determining the fair value of investments)

The inputs or methodology used for valuing securities are not necessarily an indication of the credit risk associated with investing in those securities. The following table provides the fair value measurements of applicable Company assets and liabilities that are measured at fair value on a recurring basis according to the fair value levels described above as of March 31, 2013 and December 31, 2012.

9

	Assets and Liabilities at Fair Value as of March 31, 2013
	Level 1		Level 2		Level 3		Total
	(in thousands)
Assets
Cash and cash equivalents	$	34,248	$	—	$	—	$	34,248
Short-term investments	162,915		—		—		162,915
Total cash and cash equivalents and investments	$	197,163	$	—	$	—	$	197,163
Liabilities
Other long-term liabilities	$	—	$	—	$	31,184	$	31,184
Total liabilities	$	—	$	—	$	31,184	$	31,184

	Assets and Liabilities at Fair Value as of December 31, 2012
	Level 1		Level 2		Level 3		Total
	(in thousands)
Assets
Cash and cash equivalents	$	30,423	$	—	$	—	$	30,423
Short-term investments	192,785		—		—		192,785
Total cash and cash equivalents and investments	$	223,208	$	—	$	—	$	223,208
Liabilities
Other long-term liabilities	$	—	$	—	$	29,920	$	29,920
Total liabilities	$	—	$	—	$	29,920	$	29,920

The Company's Level 3 liabilities are estimated using a probability-based income approach utilizing an appropriate discount rate. Subsequent changes in the fair value of the Symphony Icon purchase consideration liability are recorded as an increase or decrease in Symphony Icon purchase liability expense in the accompanying consolidated statements of comprehensive loss. On July 30, 2012, Lexicon issued 13,237,519 shares of common stock to designees of Symphony Icon Holdings LLC ("Holdings") in satisfaction of the $35 million base payment obligation (see Note 7, Arrangements with Symphony Icon, Inc., for more information). The following table summarizes the change in consolidated balance sheet carrying value associated with Level 3 liabilities for the three months ended March 31, 2013 and 2012.

	Other Long-term Liabilities
	(in thousands)
Balance at December 31, 2012	$	29,920
Change in valuation of purchase consideration payable to former Symphony Icon stockholders	1,264
Balance at March 31, 2013	$	31,184
Balance at December 31, 2011	$	55,033
Change in valuation of purchase consideration payable to former Symphony Icon stockholders	2,081
Balance at March 31, 2012	$	57,114

The Company also has assets that under certain conditions are subject to measurement at fair value on a non-recurring basis. These assets include goodwill associated with the acquisitions of Coelacanth Corporation in 2001 and Symphony Icon on July 30, 2010 and intangible assets associated with the acquisition of Symphony Icon on July 30, 2010. For these assets, measurement at fair value in periods subsequent to their initial recognition is applicable if one or more is determined to be impaired.

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6.      Debt Obligations

Mortgage Loan.  In April 2004, Lexicon obtained a $34.0 million mortgage on its facilities in The Woodlands, Texas.  The mortgage loan has a ten-year term with a 20-year amortization and bears interest at a fixed rate of 8.23%.  The mortgage had a principal balance outstanding of $23.1 million as of March 31, 2013. The fair value of Lexicon’s mortgage loan approximates its carrying value.  The fair value of Lexicon’s mortgage loan is estimated using discounted cash flow analysis, based on the Company’s current incremental borrowing rate.

7.      Arrangements with Symphony Icon, Inc.

On June 15, 2007, Lexicon entered into a series of related agreements providing for the financing of the clinical development of certain of its drug candidates, including LX1032 and LX1033, along with any other pharmaceutical compositions modulating the same targets as those drug candidates (the “Programs”). The agreements included a Novated and Restated Technology License Agreement pursuant to which the Company licensed to Symphony Icon, a then wholly-owned subsidiary of Holdings, the Company's intellectual property rights related to the Programs. Holdings contributed $45 million to Symphony Icon in order to fund the clinical development of the Programs.

Under a Share Purchase Agreement, dated June 15, 2007, between the Company and Holdings, the Company issued and sold to Holdings 7,650,622 shares of its common stock on June 15, 2007 in exchange for $15 million and an exclusive purchase option (the "Purchase Option") that gave the Company the right to acquire all of the equity of Symphony Icon, thereby allowing the Company to reacquire all of the Programs. On July 30, 2010, Lexicon entered into an Amended and Restated Purchase Option Agreement with Symphony Icon and Holdings and simultaneously exercised the Purchase Option, thereby reacquiring the Programs. Pursuant to the amended terms of the Purchase Option, Lexicon paid Holdings $10 million on July 30, 2010 and issued 13,237,519 shares of common stock to designees of Holdings on July 30, 2012 in satisfaction of an additional $35 million base payment obligation.

Lexicon also agreed to make up to $45 million in additional contingent payments, which will consist of 50% of any consideration Lexicon receives pursuant to any licensing transaction (a “Licensing Transaction”) under which Lexicon grants a third party rights to commercialize LX1032, LX1033 or other pharmaceutical compositions modulating the same target as those drug candidates (the “LG103 Programs”), subject to certain exceptions. The contingent payments will be due if and when Lexicon receives such consideration from a Licensing Transaction. In the event Lexicon receives regulatory approval in the United States for the marketing and sale of any product resulting from the LG103 Programs prior to entering into a Licensing Transaction for the commercialization of such product in the United States, in lieu of any contingent payment from such a Licensing Transaction, Lexicon will pay Holdings the sum of $15 million and the amount of certain expenses Lexicon incurred after its exercise of the Purchase Option which are attributable to the development of such product, reduced by up to 50% of such sum for the amount of any contingent payments paid prior to such United States regulatory approval attributable to any such Licensing Transaction outside of the United States with respect to such product. In the event Lexicon makes any such payment upon United States regulatory approval, Lexicon will have no obligation to make subsequent contingent payments attributable to any such Licensing Transactions for the commercialization of such product outside the United States until the proceeds of such Licensing Transactions exceed 50% of the payment made as a result of such United States regulatory approval. The contingent payments may be paid in cash or a combination of cash and common stock, in Lexicon's discretion, provided that no more than 50% of any contingent payment will be paid in common stock.

Lexicon accounted for the exercise of the Purchase Option and acquisition of Symphony Icon as a business combination. In connection with its acquisition of Symphony Icon, Lexicon paid $10.0 million in cash, and also agreed to pay Holdings additional base and contingent payments as discussed above. The fair value of the base and contingent consideration payments was $45.6 million at the date of acquisition and was estimated by applying a probability-based income approach utilizing an appropriate discount rate. This estimation was based on significant inputs that are not observable in the market, referred to as Level 3 inputs. Key assumptions include: (1) a discount rate of 14% for the base payments; (2) a discount rate of 18% for the contingent payments; and (3) a probability adjusted contingency. The discount rate assumptions have not changed through March 31, 2013, and as programs progress, the probability adjusted contingency is adjusted as necessary. Subsequent changes in the fair value of the Symphony Icon purchase consideration liability are recorded as an increase or decrease in fair value of Symphony Icon purchase liability expense in the accompanying consolidated statements of comprehensive loss. During the three months ended March 31, 2013 and 2012, the fair value of the Symphony Icon purchase consideration liability increased by $1.3 million and $2.1 million, respectively.

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8.      Commitments and Contingencies

Operating Lease Obligations:  A Lexicon subsidiary leases laboratory and office space in Hopewell, New Jersey under an agreement which expires in June 2018.  Rent expense is recognized on a straight-line basis over the lease term.  Lexicon is the guarantor of the obligations of its subsidiary under this lease.  The maximum potential amount of future payments the Company could be required to make under this agreement is $5.3 million as of March 31, 2013. The Company is required to maintain restricted investments to collateralize a standby letter of credit for this lease.  The Company had $0.4 million and $0.4 million in restricted investments as collateral as of March 31, 2013 and December 31, 2012, respectively.  Additionally, Lexicon leases certain equipment under operating leases.

Legal Proceedings.  Lexicon is from time to time party to claims and legal proceedings that arise in the normal course of its business and that it believes will not have, individually or in the aggregate, a material adverse effect on its results of operations, financial condition or liquidity.

9.      Collaboration and License Agreements

Lexicon has derived substantially all of its revenues from drug discovery and development collaborations, target validation collaborations for the development and, in some cases, analysis of the physiological effects of genes altered in knockout mice, government grants and contracts, technology licenses, subscriptions to its databases and compound library sales. Revenues generated from third parties under collaborative arrangements are recorded on a gross basis on the consolidated statements of comprehensive loss as Lexicon is the principal participant for these transactions for the purpose of accounting for these arrangements.

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Item 2. Management's Discussion and Analysis of Financial Condition and Results of Operations

Overview

We are a biopharmaceutical company focused on the discovery and development of breakthrough treatments for human disease. We have used gene knockout technologies and an integrated platform of advanced medical technologies to identify and validate, in vivo, more than 100 targets with promising profiles for drug discovery. For targets that we believe have high pharmaceutical value, we engage in programs for the discovery and development of potential new drugs. We have multiple drug programs in various stages of clinical development and have advanced small molecule compounds from a number of additional drug programs into various stages of preclinical development and research.

We are working both independently and through strategic collaborations and alliances to capitalize on our technology, drug target discoveries and drug discovery and development programs. Consistent with this approach, we seek to retain exclusive rights to the benefits of certain drug programs by developing drug candidates from those programs internally and to collaborate with third parties with respect to the discovery, development and commercialization of drug candidates for other targets, particularly when the collaboration provides us with access to expertise and resources that we do not possess internally or are complementary to our own. We have established drug discovery and development collaborations with leading pharmaceutical and biotechnology companies which generated near-term cash while offering us the potential to retain economic participation in products developed from the collaboration. In addition, we have established collaborations and license agreements with other leading pharmaceutical and biotechnology companies, research institutes and academic institutions under which we received fees and, in some cases, are eligible to receive milestone and royalty payments, in return for granting access to some of our technologies and discoveries.

We have derived substantially all of our revenues from drug discovery and development collaborations and other collaborations and technology licenses, and will continue to do so for the foreseeable future. To date, we have generated a substantial portion of our revenues from a limited number of sources.    

Our operating results and, in particular, our ability to generate additional revenues are dependent on many factors, including our success in establishing new collaborations and licenses, the success rate of our discovery and development efforts leading to opportunities for new collaborations and licenses, the timing and willingness of collaborators to commercialize products that would result in milestone payments and royalties and their success in such efforts, and general and industry-specific economic conditions which may affect research and development expenditures. Future revenues from our existing collaborations and licenses are uncertain because they depend, to a large degree, on the achievement of milestones and payment of royalties we earn from any future products developed under the collaboration. As a result, we depend, in part, on securing new collaborations and license agreements. Our ability to secure future revenue-generating agreements will depend upon our ability to address the needs of our potential future collaborators and licensees, and to negotiate agreements that we believe are in our long-term best interests. We may determine, as we have with certain of our clinical drug candidates, that our interests are better served by retaining rights to our discoveries and advancing our therapeutic programs to a later stage, which could limit our near-term revenues. Because of these and other factors, our operating results have fluctuated in the past and are likely to do so in the future, and we do not believe that period-to-period comparisons of our operating results are a good indication of our future performance.

Since our inception, we have incurred significant losses and, as of March 31, 2013, we had an accumulated deficit of $925.8 million. Our losses have resulted principally from costs incurred in research and development, general and administrative costs associated with our operations, and non-cash stock-based compensation expenses associated with stock options and restricted stock granted to employees and consultants. Research and development expenses consist primarily of salaries and related personnel costs, external research costs related to our preclinical and clinical efforts, material costs, facility costs, depreciation on property and equipment, and other expenses related to our drug discovery and development programs. General and administrative expenses consist primarily of salaries and related expenses for executive and administrative personnel, professional fees and other corporate expenses, including information technology, facilities costs and general legal activities. We expect to continue to incur significant research and development costs in connection with our drug discovery and development programs. As a result, we will need to generate significantly higher revenues to achieve profitability.

Critical Accounting Policies

The preparation of financial statements in conformity with generally accepted accounting principles requires us to make judgments, estimates and assumptions in the preparation of our consolidated financial statements and accompanying

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notes.  Actual results could differ from those estimates.  We believe there have been no significant changes in our critical accounting policies as discussed in our Annual Report on Form 10-K for the year ended December 31, 2012.

Recent Accounting Pronouncements

There are no recent accounting pronouncements that have a material impact on our consolidated financial statements.

Results of Operations

Revenues

Total revenues and dollar and percentage changes as compared to the corresponding period in the prior year are as follows (dollar amounts are presented in millions):

	Three Months Ended March 31,
	2013			2012
Total revenues	$	0.4		$	0.3
Dollar increase	$	0.1
Percentage increase	20		%

• Collaborative research – Revenue from collaborative research for the three months ended March 31, 2013 increased 87% to $0.3 million, as compared to the corresponding period in 2012, primarily due to increased revenues under our alliance with Taconic Farms.

• Subscription and license fees – Revenue from subscriptions and license fees for the three months ended March 31, 2013 decreased 49% to $0.1 million, as compared to the corresponding period in 2012, primarily due to a decrease in technology license fees.

Research and Development Expenses

Research and development expenses and dollar and percentage changes as compared to the corresponding period in the prior year are as follows (dollar amounts are presented in millions):

	Three Months Ended March 31,
	2013			2012
Total research and development expense	$	20.3		$	23.0
Dollar decrease	$	(2.7	)
Percentage decrease	(12		)%

Research and development expenses consist primarily of salaries and other personnel-related expenses, third-party and other services principally related to preclinical and clinical development activities, facility and equipment costs, stock-based compensation expense, and laboratory supplies costs.

• Personnel – Personnel costs for the three months ended March 31, 2013 decreased 9% to $7.3 million, as compared to the corresponding period in 2012, primarily due to reductions in our personnel in January 2012. Salaries, bonuses, employee benefits, payroll taxes, recruiting and relocation costs are included in personnel costs.

• Third-party and other services – Third-party and other services for the three months ended March 31, 2013 decreased 19% to $7.2 million, as compared to the corresponding period in 2012, primarily due to decreases in external preclinical and clinical research and development costs. Third-party and other services relate principally to our clinical trial and related development activities, such as preclinical and clinical studies and contract manufacturing.

• Facilities and equipment – Facilities and equipment costs for the three months ended March 31, 2013 decreased 25% to $2.2 million, as compared to the corresponding period in 2012, primarily due to decreases in rent costs and depreciation expense. Effective December 31, 2012, our subsidiary Lexicon Pharmaceuticals (New Jersey), Inc. amended its laboratory and office space lease extending the lease term and decreasing both the rentable square-feet and rental rate.

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• Stock-based compensation – Stock-based compensation expense for the three months ended March 31, 2013 increased 28% to $1.3 million, as compared to the corresponding period in 2012.

• Laboratory supplies – Laboratory supplies expense for the three months ended March 31, 2013 decreased 9% to

$0.8 million, as compared to the corresponding period in 2012, primarily due to reductions in early-stage research activities.

• Other – Other costs for the three months ended March 31, 2013 increased 15% to $1.5 million, as compared to the corresponding period in 2012.

Increase in Fair Value of Symphony Icon Liability

The increase in fair value of the Symphony Icon purchase liability was $1.3 million and $2.1 million for the three months ended March 31, 2013 and 2012, respectively (see Note 7, Arrangements with Symphony Icon, Inc., of the Notes to Consolidated Financial Statements, for more information).

General and Administrative Expenses

General and administrative expenses and dollar and percentage changes as compared to the corresponding period in the prior year are as follows (dollar amounts are presented in millions):

	Three Months Ended March 31,
	2013			2012
Total general and administrative expense	$	4.3		$	4.6
Dollar decrease	$	(0.2	)
Percentage decrease	(5		)%

General and administrative expenses consist primarily of salaries and other personnel-related expenses, stock-based compensation expenses, professional fees such as legal fees, and facility and equipment costs.

• Personnel – Personnel costs for the three months ended March 31, 2013 decreased 12% to $2.1 million, as compared to the corresponding period in 2012, primarily due to reductions in our personnel in January 2012. Salaries, bonuses, employee benefits, payroll taxes, recruiting and relocation costs are included in personnel costs.

• Stock-based compensation – Stock-based compensation expense for the three months ended March 31, 2013 increased 14% to $0.8 million, as compared to the corresponding period in 2012.

• Professional fees – Professional fees for the three months ended March 31, 2013 were $0.7 million, consistent with the corresponding period in 2012.

• Facilities and equipment – Facilities and equipment costs for the three months ended March 31, 2013 decreased 16% to $0.4 million, as compared to the corresponding period in 2012.

• Other – Other costs for the three months ended March 31, 2013 were $0.3 million, consistent with the corresponding period in 2012.

Interest Income and Interest Expense

Interest Income.  Interest income for the three months ended March 31, 2013 was $0.1 million, consistent with the corresponding period in 2012.

Interest Expense.  Interest expense for the three months ended March 31, 2013 was $0.5 million, consistent with the corresponding period in 2012.

Consolidated Net Loss and Consolidated Net Loss per Common Share

Consolidated Net Loss and Consolidated Net Loss per Common Share. Consolidated net loss decreased to $26.0 million in the three months ended March 31, 2013 from $29.9 million in the corresponding period in 2012. Consolidated

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net loss per common share decreased to $0.05 in the three months ended March 31, 2013 from $0.06 in the corresponding period in 2012.

Our quarterly operating results have fluctuated in the past and are likely to do so in the future, and we believe that quarter-to-quarter comparisons of our operating results are not a good indication of our future performance.

Liquidity and Capital Resources

We have financed our operations from inception primarily through sales of common and preferred stock, contract and milestone payments to us under our drug discovery and development collaborations, target validation, database subscription and technology license agreements, government grants and contracts, and financing obtained under debt and lease arrangements. We have also financed certain of our research and development activities under our agreements with Symphony Icon, Inc. From our inception through March 31, 2013, we had received net proceeds of $986.0 million from issuances of common and preferred stock. In addition, from our inception through March 31, 2013, we received $456.4 million in cash payments from drug discovery and development collaborations, target validation, database subscription and technology license agreements, sales of compound libraries and reagents, and government grants and contracts, of which $442.9 million had been recognized as revenues through March 31, 2013.

As of March 31, 2013, we had $197.2 million in cash, cash equivalents and investments. As of December 31, 2012, we had $223.2 million in cash, cash equivalents and investments. We used cash of $24.3 million in operations in the three months ended March 31, 2013. This consisted primarily of the consolidated net loss for the period of $26.0 million and a net increase in other operating assets net of liabilities of $2.5 million, partially offset by non-cash charges of $2.1 million related to stock-based compensation expense, $1.3 million related to the increase in fair value of the Symphony Icon purchase liability and $0.8 million related to depreciation expense. Investing activities provided cash of $29.1 million in the three months ended March 31, 2013, primarily due to net maturities of investments of $29.9 million, partially offset by purchases of property and equipment of $0.8 million. Financing activities used cash of $1.0 million primarily due to repurchase of common stock of $0.9 million and repayment of debt borrowings of $0.4 million, partially offset by proceeds of $0.2 million related to issuance of common stock.

Symphony Drug Development Financing Agreements. In June 2007, we entered into a series of related agreements providing for the financing of the clinical development of certain drug programs, including LX1032 and LX1033, along with any other pharmaceutical compositions modulating the same targets as those drug candidates. Under the financing arrangement, we licensed to Symphony Icon, Inc., a then wholly-owned subsidiary of Symphony Icon Holdings LLC, our intellectual property rights related to the programs and Holdings contributed $45 million to Symphony Icon in order to fund the clinical development of the programs. We also issued and sold to Holdings shares of our common stock in exchange for $15 million and received an exclusive option to acquire all of the equity of Symphony Icon, thereby allowing us to reacquire the programs.

Upon the recommendation of Symphony Icon's development committee, which was comprised of an equal number of representatives from us and Symphony Icon, Symphony Icon's board of directors had the right to require us to pay Symphony Icon up to $15 million for Symphony Icon's use in the development of the programs in accordance with the specified development plan and related development budget. Through July 2010, Symphony Icon's board of directors requested us to pay Symphony Icon $9.3 million under the agreement, all of which was paid prior to the exercise of the purchase option in July 2010.

In July 2010, we entered into an amended and restated purchase option agreement with Symphony Icon and Holdings and simultaneously exercised our purchase option. Pursuant to the amended terms of the purchase option, we paid Holdings $10 million in July 2010 and issued 13,237,519 shares of common stock to designees of Holdings in July 2012 in satisfaction of an additional $35 million base payment obligation.

We also agreed to make up to $45 million in additional contingent payments, which will consist of 50% of any consideration we receive pursuant to any licensing transaction under which we grant a third party rights to commercialize LX1032, LX1033 or other pharmaceutical compositions modulating the same target as those drug candidates, which we refer to as the “LG103 programs,” subject to certain exceptions. The contingent payments will be due if and when we receive such consideration from such a licensing transaction. In the event we receive regulatory approval in the United States for the marketing and sale of any product resulting from the LG103 programs prior to entering into such a licensing transaction for the commercialization of such product in the United States, in lieu of any contingent payment from such a licensing transaction, we will pay Holdings the sum of $15 million and the amount of certain expenses we incurred after our exercise of the purchase option which are attributable to the development of such product, reduced by up to 50% of such sum for the amount of any contingent payments paid prior to such United States regulatory approval attributable to any such licensing transaction outside

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of the United States with respect to such product. In the event we make any such payment upon United States regulatory approval, we will have no obligation to make subsequent contingent payments attributable to any such licensing transactions for the commercialization of such product outside the United States until the proceeds of such licensing transactions exceed 50% of the payment made as a result of such United States regulatory approval.

The contingent payments may be paid in cash or a combination of cash and common stock, in our discretion, provided that no more than 50% of any contingent payment will be paid in common stock.

Texas Institute for Genomic Medicine. In July 2005, we received an award from the Texas Enterprise Fund for the

creation of a knockout mouse embryonic stem cell library containing 350,000 cell lines for the Texas Institute for Genomic

Medicine, or TIGM, using our proprietary gene trapping technology, which we completed in 2007. We also equipped TIGM

with the bioinformatics software required for the management and analysis of data relating to the library. The Texas Enterprise Fund made an additional award to the Texas A&M University System for the creation of facilities and infrastructure to house

the library.

Under the terms of our award, we are responsible for the creation of a specified number of jobs beginning in 2012,

reaching an aggregate of 1,616 new jobs in Texas by December 31, 2016. We will receive credits against those job obligations

based on funding received by TIGM and certain related parties from sources other than the State of Texas. We will also receive

credits against those jobs obligations for any surplus jobs we create. We may be required to repay the state a portion of the

award if we fail to meet those job obligations. Subject to these credits, if we fail to create the specified number of jobs, the

State may require us to repay $2,415 for each job we fall short beginning in 2013. Our maximum aggregate exposure for such

payments, if we fail to create any new jobs, is approximately $14.2 million, without giving effect to any credits to which we

may be entitled.

Facilities. In April 2004, we obtained a $34.0 million mortgage on our facilities in The Woodlands, Texas. The mortgage loan has a ten-year term with a 20-year amortization and bears interest at a fixed rate of 8.23%. The mortgage had a principal balance outstanding of $23.1 million as of March 31, 2013. A balloon payment of $21.4 million is due in April 2014.

In May 2002, our subsidiary Lexicon Pharmaceuticals (New Jersey), Inc. leased a 76,000 square-foot laboratory and office space in Hopewell, New Jersey. Effective December 31, 2012, this lease was amended to decrease the space to approximately 42,000 square feet. The term of the amended lease extends until June 30, 2018. The amended lease provides for escalating yearly base rent payments starting at $836,000 and increasing to $941,000 in the final year of the lease. We are the guarantor of the obligations of our subsidiary under the lease.

Our future capital requirements will be substantial and will depend on many factors, including our ability to obtain drug discovery and development collaborations and other collaborations and technology license agreements, the amount and timing of payments under such agreements, the level and timing of our research and development expenditures, market acceptance of our products, the resources we devote to developing and supporting our products and other factors. Our capital requirements will also be affected by any expenditures we make in connection with license agreements and acquisitions of and investments in complementary technologies and businesses. We expect to devote substantial capital resources to continue our research and development efforts, to expand our support and product development activities, and for other general corporate activities. We believe that our current unrestricted cash and investment balances and cash and revenues we expect to derive from drug discovery and development collaborations, other collaborations and technology licenses and other sources will be sufficient to fund our operations for at least the next 12 months. During or after this period, if cash generated by operations is insufficient to satisfy our liquidity requirements, we will need to sell additional equity or debt securities or obtain additional credit arrangements. Additional financing may not be available on terms acceptable to us or at all. The sale of additional equity or convertible debt securities may result in additional dilution to our stockholders.

Disclosure about Market Risk

We are exposed to limited market and credit risk on our cash equivalents which have maturities of three months or less

at the time of purchase. We maintain a short-term investment portfolio which consists of U.S. Treasury bills, money market accounts, and certificates of deposit that mature three to 12 months from the time of purchase, which we believe are subject to limited market and credit risk. We currently do not hedge interest rate exposure or hold any derivative financial instruments in our investment portfolio.

We had approximately $197.2 million in cash and cash equivalents and short-term investments as of March 31, 2013. We believe that the working capital available to us will be sufficient to meet our cash requirements for at least the next 12 months.

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We have operated primarily in the United States and substantially all sales to date have been made in U.S. dollars. Accordingly, we have not had any material exposure to foreign currency rate fluctuations.

Item 3.                 Quantitative and Qualitative Disclosures About Market Risk

See “Disclosure about Market Risk” under “Item 2. Management’s Discussion and Analysisof Financial Condition and Results of Operations” for quantitative and qualitative disclosures about market risk.

Item 4.                 Controls and Procedures

Our principal executive officer and principal financial officer have concluded that our disclosure controls and procedures (as defined in rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934) are effective to ensure that the information required to be disclosed by us in the reports we file under the Securities Exchange Act is gathered, analyzed and disclosed with adequate timeliness, accuracy and completeness, based on an evaluation of such controls and procedures as of the end of the period covered by this report.

Subsequent to our evaluation, there were no significant changes in internal controls or other factors that could significantly affect internal controls, including any corrective actions with regard to significant deficiencies and material weaknesses.

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Part II -- Other Information 

Item 1. Legal Proceedings

We are from time to time party to claims and legal proceedings that arise in the normal course of our business and that we believe will not have, individually or in the aggregate, a material adverse effect on our results of operations, financial condition or liquidity.

Item 1A.   Risk Factors

The following risks and uncertainties are important factors that could cause actual results or events to differ materially from those indicated by forward-looking statements. The factors described below are not the only ones we face and additional risks and uncertainties not presently known to us or that we currently deem immaterial also may impair our business operations.

Risks Related to Our Need for Additional Financing and Our Financial Results

• We will need additional capital in the future and, if it is unavailable, we will be forced to significantly curtail or cease our operations. If it is not available on reasonable terms, we will be forced to obtain funds by entering into financing agreements on unattractive terms.

• We have a history of net losses, and we expect to continue to incur net losses and may not achieve or maintain profitability.

• Our operating results have been and likely will continue to fluctuate, and we believe that period-to-period comparisons of our operating results are not a good indication of our future performance.

Risks Related to Discovery and Development of Our Drug Candidates

• We have not proven our ability to successfully develop and commercialize drug candidates based on our drug target discoveries.

• Clinical testing of our drug candidates in humans is an inherently risky and time-consuming process that may fail to demonstrate safety and efficacy, which could result in the delay, limitation or prevention of regulatory approval.

Risks Related to Regulatory Approval of Our Drug Candidates

• Our drug candidates are subject to a lengthy and uncertain regulatory process that may not result in the necessary regulatory approvals, which could adversely affect our ability to commercialize products.

• If our potential products receive regulatory approval, we or our collaborators will remain subject to extensive and rigorous ongoing regulation.

Risks Related to Commercialization of Products

• The commercial success of any products that we may develop will depend upon the degree of market acceptance of our products among physicians, patients, health care payors, private health insurers and the medical community.

• If we are unable to establish sales and marketing capabilities or enter into agreements with third parties to market and sell our drug candidates, we may be unable to generate product revenues.

• If we are unable to obtain adequate coverage and reimbursement from third-party payors for any products that we may develop, our revenues and prospects for profitability will suffer.

• Current and future healthcare laws and regulations may negatively affect our revenues and prospects for profitability.

• Our competitors may develop products that make our products obsolete.

• We may not be able to manufacture our drug candidates in commercial quantities, which would prevent us from commercializing our drug candidates.

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Risks Related to Our Relationships with Third Parties

• We are dependent in many ways upon our collaborations with major pharmaceutical companies. If we are unable to establish new collaborations, if milestones are not achieved under our collaborations or if our collaborators' efforts fail to yield pharmaceutical products on a timely basis, our opportunities to generate revenues and earn royalties will be reduced.

• Conflicts with our collaborators could jeopardize the success of our collaborative agreements and harm our product development efforts.

• We rely on third parties to carry out drug development activities.

• We lack the capability to manufacture materials for preclinical studies, clinical trials or commercial sales and rely on third parties to manufacture our drug candidates, which may harm or delay our product development and commercialization efforts.

Risks Related to Our Intellectual Property

• If we are unable to adequately protect our intellectual property, third parties may be able to use our products and technologies, which could adversely affect our ability to compete in the market.

• We may be involved in patent litigation and other disputes regarding intellectual property rights and may require licenses from third parties for our discovery and development and planned commercialization activities. We may not prevail in any such litigation or other dispute or be able to obtain required licenses.

• We use intellectual property that we license from third parties. If we do not comply with these licenses, we could lose our rights under them.

• We have not sought patent protection outside of the United States for some of our inventions, and some of our licensed patents only provide coverage in the United States. As a result, our international competitors could be granted foreign patent protection with respect to our discoveries.

• We may be subject to damages resulting from claims that we, our employees or independent contractors have wrongfully used or disclosed alleged trade secrets of their former employers.

Risks Related to Employees, Advisors and Facilities Operations

• The loss of key personnel or the inability to attract and retain additional personnel could impair our ability to expand our operations.

• Our collaborations with outside scientists may be subject to restriction and change.

• Because most of our operations are located at a limited number of locations, the occurrence of a disaster could significantly disrupt our business.

Risks Related to Environmental and Product Liability

• We use hazardous chemicals and radioactive and biological materials in our business. Any claims relating to improper handling, storage or disposal of these materials could be time consuming and costly.

• We may be sued for product liability.

Risks Related to Our Common Stock

• Invus, L.P., Invus C.V. and their affiliates own a controlling interest in our outstanding common stock and may have interests which conflict with those of our other stockholders.

• Invus has additional rights under our stockholders' agreement with Invus, L.P. which provides Invus with substantial influence over certain significant corporate matters.

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• Our stock price may be extremely volatile.

• We may engage in future acquisitions, which may be expensive and time consuming and from which we may not realize anticipated benefits.

• Future sales of our common stock may depress our stock price.

• If we are unable to meet Nasdaq continued listing requirements, Nasdaq may take action to delist our common stock.

For additional discussion of the risks and uncertainties that affect our business, see “Item 1A. Risk Factors” included in our annual report on Form 10-K for the year ended December 31, 2012 as filed with the Securities and Exchange Commission.

Item 2.Unregistered Sales of Equity Securities and Use of Proceeds

The following table provides information about our purchases of shares of our common stock during the three months ended March 31, 2013:

Period	Total Number of Shares Purchased		Average Price Paid Per Share			Total Number of Shares Purchased as Part of Publicly Announced Plans or Programs	Maximum Number of Shares that May Yet be Purchased Under the Plans or Programs(4)
January 1-31, 2013	109,345	(1)	$	2.11	(3)	—	—
February 1-28, 2013	324,401	(2)	$	1.98	(3)	—	—
March 1-31, 2013	—		$	—		—	—

(1) Represents shares retained by us in satisfaction of the tax withholding obligations of recipients of restricted stock units granted in February 2010 under our Equity Incentive Plan with respect to the vesting of such restricted stock units.

(2) Represents shares retained by us in satisfaction of the tax withholding obligations of recipients of restricted stock units granted in February 2011 and February 2012 under our Equity Incentive Plan with respect to the vesting of such restricted stock units.

(3) Represents the market price of our common stock on the date of vesting of such restricted stock units, calculated in accordance with the process for determination of fair market value under our Equity Incentive Plan.

(4) In the future, we may grant additional equity securities under our Equity Incentive Plan for which the recipient's tax withholding obligations with respect to the grant or vesting of such securities may be satisfied by our retention of a portion of such securities. Further, for any such equity securities which are subject to vesting conditions, the number of equity securities which we may retain in satisfaction of the recipient's tax withholding obligations may be dependent on the continued employment of such recipient or other performance-based conditions. Accordingly, we cannot predict with any certainty either the total amount of equity securities or the approximate dollar value of such securities that we may purchase in future years.

Item 6. Exhibits

Exhibit No.		Description
31.1	—	Certification of Principal Executive Officer Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002
31.2	—	Certification of Principal Financial Officer Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002
32.1	—	Certification of Principal Executive and Principal Financial Officers Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002
101.INS	—	XBRL Instance Document
101.SCH	—	XBRL Taxonomy Extension Schema Document
101.CAL	—	XBRL Taxonomy Extension Calculation Linkbase Document
101.DEF	—	XBRL Taxonomy Extension Definition Linkbase Document
101.LAB	—	XBRL Taxonomy Extension Label Linkbase Document
101.PRE	—	XBRL Taxonomy Extension Presentation Linkbase Document

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Signatures

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.

		Lexicon Pharmaceuticals, Inc.
Date:	May 10, 2013	By:	/s/ Arthur T. Sands
			Arthur T. Sands, M.D., Ph.D.
			President and Chief Executive Officer

Date:	May 10, 2013	By:	/s/ Jeffrey L. Wade
			Jeffrey L. Wade
			Executive Vice President, Corporate Development and Chief Financial Officer

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Index to Exhibits

Exhibit No.		Description
31.1	—	Certification of Principal Executive Officer Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002
31.2	—	Certification of Principal Financial Officer Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002
32.1	—	Certification of Principal Executive and Principal Financial Officers Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002
101.INS	—	XBRL Instance Document
101.SCH	—	XBRL Taxonomy Extension Schema Document
101.CAL	—	XBRL Taxonomy Extension Calculation Linkbase Document
101.DEF	—	XBRL Taxonomy Extension Definition Linkbase Document
101.LAB	—	XBRL Taxonomy Extension Label Linkbase Document
101.PRE	—	XBRL Taxonomy Extension Presentation Linkbase Document

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EX-31.1

Exhibit 31.1

CERTIFICATIONS

I, Arthur T. Sands, certify that:

1. I have reviewed this Quarterly Report on Form 10-Q of Lexicon Pharmaceuticals, Inc.;

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4. The registrant's other certifying officers and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

a) designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b) designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c) evaluated the effectiveness of the registrant's disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d) disclosed in this report any change in the registrant's internal control over financial reporting that occurred during the registrant's most recent fiscal quarter (the registrant's fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant's internal control over financial reporting; and

5. The registrant's other certifying officers and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant's auditors and the audit committee of the registrant's board of directors (or persons performing the equivalent functions):

a) all significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant's ability to record, process, summarize and report financial information; and

b) any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant's internal control over financial reporting.

Date: May 8, 2013

/s/ Arthur T. Sands

Arthur T. Sands, M.D., Ph.D.

President and Chief Executive Officer

EX-31.2

Exhibit 31.2

CERTIFICATIONS

I, Jeffrey L. Wade, certify that:

1. I have reviewed this Quarterly Report on Form 10-Q of Lexicon Pharmaceuticals, Inc.;

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4. The registrant's other certifying officers and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

a) designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b) designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c) evaluated the effectiveness of the registrant's disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d) disclosed in this report any change in the registrant's internal control over financial reporting that occurred during the registrant's most recent fiscal quarter (the registrant's fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant's internal control over financial reporting; and

5. The registrant's other certifying officers and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant's auditors and the audit committee of the registrant's board of directors (or persons performing the equivalent functions):

a) all significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant's ability to record, process, summarize and report financial information; and

b) any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant's internal control over financial reporting.

Date: May 8, 2013

/s/ Jeffrey L. Wade

Jeffrey L. Wade

Executive Vice President, Corporate Development and

Chief Financial Officer

EX-32.1

Exhibit 32.1

CERTIFICATION

Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002 (18 U.S.C. 1350, as adopted), Arthur T. Sands, M.D., Ph.D., Principal Executive Officer of Lexicon Pharmaceuticals, Inc. (“Lexicon”), and Jeffrey L. Wade, Principal Financial Officer of Lexicon, each hereby certify that:

1. Lexicon's Quarterly Report on Form 10-Q for the period ended March 31, 2013, and to which this Certification is attached as Exhibit 32.1 (the “Periodic Report”), fully complies with the requirements of section 13(a) or section 15(d) of the Securities Exchange Act of 1934, and

2. The information contained in the Periodic Report fairly presents, in all material respects, the financial condition and results of operations of Lexicon.

IN WITNESS WHEREOF, the undersigned have set their hands hereto as of the 8th day of May, 2013.

By:	/s/ Arthur T. Sands
	Arthur T. Sands, M.D., Ph.D.
	President and Chief Executive Officer

By:	/s/ Jeffrey L. Wade
	Jeffrey L. Wade
	Executive Vice President, Corporate Development and Chief Financial Officer

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Commitments and Contingencies (Details) (USD $)	Mar. 31, 2013	Dec. 31, 2012
Operating Leased Assets [Line Items]
Guarantor Obligations, Maximum Exposure, Undiscounted	$ 5,300,000
Restricted investments	$ 430,000	$ 430,000

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Stock-Based Compensation (Details 5) (Performance Stock Units (PSUs) [Member], USD $) In Thousands, except Per Share data, unless otherwise specified	3 Months Ended
	Mar. 31, 2013	Dec. 31, 2012
Performance Stock Units (PSUs) [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Performance stock units	0	329
Performance stock units, weighted-average grant date fair value	$ 0.00	$ 1.90
Performance stock units vested	(329)
Performance stock units vested, weighted-average grant date fair value	$ 1.90

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Net Loss Per Share

3 Months Ended

Mar. 31, 2013

Net Loss Per Share [Abstract]

Earnings Per Share [Text Block]

Net Loss Per Share

Net loss per share is computed using the weighted average number of shares of common stock outstanding during the applicable period and excludes shares underlying stock options and restricted stock units because they are antidilutive.  There are no differences between basic and diluted net loss per share for all periods presented.

Earnings Per Share, Policy

Net loss per share is computed using the weighted average number of shares of common stock outstanding during the applicable period and excludes shares underlying stock options and restricted stock units because they are antidilutive.

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Fair Value Measurements (Details 2) (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Mar. 31, 2013	Mar. 31, 2012	Dec. 31, 2012	Dec. 31, 2011
Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation
Fair Value, Measurement with Unobservable Inputs Reconciliation, Recurring Basis, Liability, Gain (Loss) Included in Earnings	$ 1,264	$ 2,081
Fair Value, Measurement with Unobservable Inputs Reconciliations, Recurring Basis, Liability Value	$ 31,184	$ 57,114	$ 29,920	$ 55,033

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Fair Value Measurements (Details) (USD $) In Thousands, unless otherwise specified	Mar. 31, 2013	Dec. 31, 2012
Fair Value, Level 1
Fair Value
Cash and cash equivalents	$ 34,248	$ 30,423
Short-term investments	162,915	192,785
Total cash and cash equivalents and investments	197,163	223,208
Other long-term liabilities	0	0
Total liabilities	0	0
Fair Value, Level 2
Fair Value
Cash and cash equivalents	0	0
Short-term investments	0	0
Total cash and cash equivalents and investments	0	0
Other long-term liabilities	0	0
Total liabilities	0	0
Fair Value, Level 3
Fair Value
Cash and cash equivalents	0	0
Short-term investments	0	0
Total cash and cash equivalents and investments	0	0
Other long-term liabilities	31,184	29,920
Total liabilities	31,184	29,920
Fair Value, Total
Fair Value
Cash and cash equivalents	34,248	30,423
Short-term investments	162,915	192,785
Total cash and cash equivalents and investments	197,163	223,208
Other long-term liabilities	31,184	29,920
Total liabilities	$ 31,184	$ 29,920

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Fair Value Measurements (Details 3) (USD $) In Millions, except Share data, unless otherwise specified	Jul. 30, 2012
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Symphony base payment in shares	13,237,519
Symphony base payment obligation	$ 35

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Debt Obligations (Details) (USD $) In Millions, unless otherwise specified	1 Months Ended
	Apr. 30, 2004	Mar. 31, 2013
Debt Instrument [Line Items]
Mortgage Loans on Real Estate, New Mortgage Loans	$ 34.0
Debt Instrument, Interest Rate, Stated Percentage		8.23%
Secured Debt		$ 23.1

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Basis of Presentation

3 Months Ended

Mar. 31, 2013

Basis of Presentation [Abstract]

Organization, Consolidation and Presentation of Financial Statements Disclosure

Basis of Presentation

The accompanying unaudited consolidated financial statements of Lexicon Pharmaceuticals, Inc. (“Lexicon” or the “Company”) have been prepared in accordance with generally accepted accounting principles for interim financial information and pursuant to the rules and regulations of the Securities and Exchange Commission (“SEC”). Accordingly, they do not include all of the information and footnotes required by generally accepted accounting principles for complete financial statements.

In the opinion of management, all adjustments (consisting of normal recurring adjustments) considered necessary for a fair presentation have been included. Operating results for the three-month period ended March 31, 2013 are not necessarily indicative of the results that may be expected for the year ended December 31, 2013.

The accompanying consolidated financial statements include the accounts of Lexicon and its wholly-owned subsidiaries. Intercompany transactions and balances are eliminated in consolidation.

For further information, refer to the financial statements and footnotes thereto included in Lexicon’s annual report on Form 10-K for the year ended December 31, 2012, as filed with the SEC.

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Arrangements with Symphony Icon Inc (Details) (USD $)	3 Months Ended
	Mar. 31, 2013	Mar. 31, 2012	Jul. 30, 2012	Jul. 30, 2010	Jun. 15, 2007
Loss Contingencies [Line Items]
Holdings contribution to Icon					$ 45,000,000
Lexicon sold shares to Holdings					7,650,622
Lexicon received cash from Holdings					15,000,000
Lexicon paid Holdings cash				10,000,000
Symphony base payment in shares			13,237,519
Symphony base payment obligation			35,000,000
Symphony contingent payment maximum				45,000,000
Symphony contingent payment percentage				50.00%
Symphony regulatory approval payment				15,000,000
Symphony regulatory approval reduction percentage				50.00%
Symphony regulatory approval percentage limit				50.00%
Symphony payment in stock limitation				50.00%
Symphony fair value of base and contingent payments				45,600,000
Symphony base payment discount rate				14.00%
Symphony contingent payment discount rate				18.00%
Increase in fair value of Symphony Icon, Inc. purchase liability	$ 1,264,000	$ 2,081,000

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Consolidated Balance Sheets (Unaudited) (USD $) In Thousands, unless otherwise specified	Mar. 31, 2013	Dec. 31, 2012
Current assets:
Cash and cash equivalents	$ 34,248	$ 30,423
Short-term investments, including restricted investments of $430	162,915	192,785
Accounts receivable, net of allowances of $35	863	1,378
Prepaid expenses and other current assets	8,438	6,349
Total current assets	206,464	230,935
Property and equipment, net of accumulated depreciation and amortization of $80,882 and $83,416, respectively	42,623	42,634
Goodwill	44,543	44,543
Other intangible assets	53,557	53,557
Other assets	88	109
Total assets	347,275	371,778
Current liabilities:
Accounts payable	5,442	7,661
Accrued liabilities	9,704	8,922
Current portion of deferred revenue	628	128
Current portion of long-term debt	1,607	1,574
Total current liabilities	17,381	18,285
Deferred revenue, net of current portion	13,405	13,910
Long-term debt	21,457	21,877
Deferred tax liabilities	18,745	18,745
Other long-term liabilities	34,079	32,283
Total liabilities	105,067	105,100
Commitments and contingencies
Equity:
Preferred stock, $.01 par value; 5,000 shares authorized; no shares issued and outstanding	0	0
Common stock, $.001 par value; 900,000 shares authorized; 513,835 and 512,375 shares issued, respectively	514	512
Additional paid-in capital	1,168,961	1,166,605
Accumulated deficit	(925,806)	(899,832)
Accumulated other comprehensive gain	42	23
Treasury stock, at cost, 814 and 380 shares, respectively	(1,503)	(630)
Total equity	242,208	266,678
Total liabilities and equity	$ 347,275	$ 371,778

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Consolidated Statements of Stockholders' Equity (Unaudited) (USD $) In Thousands	Total	Common Stock	Additional Paid-In Capital	Accumulated Deficit	Accumulated Other Comprehensive Gain (Loss)	Treasury Stock
Balance, value at Dec. 31, 2011	$ 297,568	$ 480	$ 1,087,033	$ (789,621)	$ 21	$ (345)
Balance, shares at Dec. 31, 2011		480,389
Stock-based compensation	1,718	0	1,718	0	0	0
Issuance of common stock under Equity Incentive Plans, shares		553
Issuance of common stock under Equity Incentive Plans, value	52	1	51	0	0	0
Other	(136)	0	(136)	0	0	0
Repurchase of common stock	(285)	0	0	0	0	(285)
Net loss	(29,868)	0	0	(29,868)	0	0
Unrealized gain (loss) on investments	(78)	0	0	0	(78)	0
Balance, value at Mar. 31, 2012	268,971	481	1,088,666	(819,489)	(57)	(630)
Balance, shares at Mar. 31, 2012		480,942
Balance, value at Dec. 31, 2012	266,678	512	1,166,605	(899,832)	23	(630)
Balance, shares at Dec. 31, 2012		512,375
Stock-based compensation	2,109	0	2,109	0	0	0
Issuance of common stock under Equity Incentive Plans, shares		1,460
Issuance of common stock under Equity Incentive Plans, value	249	2	247	0	0	0
Other	0
Repurchase of common stock	(873)	0	0	0	0	(873)
Net loss	(25,974)	0	0	(25,974)	0	0
Unrealized gain (loss) on investments	19	0	0	0	19	0
Balance, value at Mar. 31, 2013	$ 242,208	$ 514	$ 1,168,961	$ (925,806)	$ 42	$ (1,503)
Balance, shares at Mar. 31, 2013		513,835

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Stock-Based Compensation (Details 2) (Stock Option [Member])	3 Months Ended
	Mar. 31, 2013	Mar. 31, 2012
Stock Option [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Expected volatility rate, employees	91.00%	92.00%
Expected volatility rate, officers and non-employee directors	81.00%	80.00%
Risk free interest rate, employees	0.80%	0.80%
Risk free interest rate, officers and non-employee directors	1.60%	1.60%
Expected term, employees	5 years	5 years
Expected term, officers and non-employee directors	8 years	8 years
Expected dividend rate, employees	0.00%	0.00%
Expected dividend rate, officers and non-employee directors	0.00%	0.00%

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Stock-Based Compensation (Details 4) (Restricted Stock Units (RSUs) [Member], USD $) In Thousands, except Per Share data, unless otherwise specified	3 Months Ended
	Mar. 31, 2013	Dec. 31, 2012
Restricted Stock Units (RSUs) [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Restricted stock units	4,484	3,543
Restricted stock units, weighted-average grant date fair value	$ 1.93	$ 1.80
Restricted stock units granted	1,969
Restricted stock units granted, weighted-average grant date fair value	$ 2.09
Restricted stock units vested	(991)
Restricted stock units vested, weighted-average grant date fair value	$ 1.80
Restricted stock units forfeited	(37)
Restricted stock units forfeited, weighted-average grant date fair value	$ 1.85

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Consolidated Statements of Cash Flows (Unaudited) (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Mar. 31, 2013	Mar. 31, 2012
Cash flows from operating activities:
Consolidated net loss	$ (25,974)	$ (29,868)
Adjustments to reconcile consolidated net loss to net cash used in operating activities:
Depreciation	793	1,125
Increase in fair value of Symphony Icon, Inc. purchase liability	1,264	2,081
Stock-based compensation	2,109	1,718
Changes in operating assets and liabilities:
Decrease in accounts receivable	515	164
Increase in prepaid expenses and other current assets	(2,089)	(1,395)
Decrease in other assets	21	24
Decrease in accounts payable and other liabilities	(905)	(851)
Decrease in deferred revenue	(5)	0
Net cash used in operating activities	(24,271)	(27,002)
Cash flows from investing activities:
Purchases of property and equipment	(839)	(234)
Proceeds from disposal of property and equipment	57	0
Purchases of investments	(80,954)	(151,776)
Maturities of investments	110,843	22,435
Net cash provided by (used in) investing activities	29,107	(129,575)
Cash flows from financing activities:
Proceeds from issuance of common stock	249	52
Repurchase of common stock	(873)	(285)
Repayment of debt borrowings	(387)	(353)
Other financing activities	0	(136)
Net cash used in financing activities	(1,011)	(722)
Net increase (decrease) in cash and cash equivalents	3,825	(157,299)
Cash and cash equivalents at beginning of period	30,423	186,309
Cash and cash equivalents at end of period	34,248	29,010
Supplemental disclosure of cash flow information:
Cash paid for interest	480	516
Supplemental disclosure of non-cash investing and financing activities:
Unrealized gain (loss) on investments	$ 19	$ (78)

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Balance Sheet Parenthetical (Parenthetical) (USD $) In Thousands, except Per Share data, unless otherwise specified	Mar. 31, 2013	Dec. 31, 2012
Restricted investments	430	430
Allowances for accounts receivable	35	35
Accumulated depreciation and amortization, property and equipment	80,882	83,416
Preferred stock, par value per share	0.01	0.01
Preferred stock, shares authorized	5,000	5,000
Preferred stock, shares issued	0	0
Preferred stock, shares outstanding	0	0
Common stock, par value per share	0.001	0.001
Common stock, shares authorized	900,000	900,000
Treasury stock, shares	814	380
Common Stock [Member]
Common stock, shares issued	513,835	512,375

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Net Loss Per Share Accounting Policies (Policies)

3 Months Ended

Mar. 31, 2013

Net Loss Per Share [Abstract]

Earnings Per Share, Policy

Net loss per share is computed using the weighted average number of shares of common stock outstanding during the applicable period and excludes shares underlying stock options and restricted stock units because they are antidilutive.

XML

Document and Entity Information Document	3 Months Ended
	Mar. 31, 2013	May 06, 2013
Document Information [Line Items]
Entity Registrant Name	LEXICON PHARMACEUTICALS, INC./DE
Entity Central Index Key	0001062822
Document Type	10-Q
Document Period End Date	Mar. 31, 2013
Amendment Flag	false
Document Fiscal Year Focus	2013
Document Fiscal Period Focus	Q1
Current Fiscal Year End Date	--12-31
Entity Current Reporting Status	Yes
Entity Filer Category	Accelerated Filer
Entity Common Stock, Shares Outstanding		513,025,272

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Stock-Based Compensation (Tables)

3 Months Ended

Mar. 31, 2013

Share-based Compensation Arrangement by Share-based Payment Award [Line Items]

Schedule of Share-based Compensation, Stock Options, Activity [Table Text Block]

	Options		Weighted Average Exercise Price
	(in thousands)
Outstanding at December 31, 2012	21,525		$	2.51
Granted	2,971		2.11
Exercised	(140	)	1.78
Expired	(695	)	3.62
Forfeited	(5	)	1.94
Outstanding at March 31, 2013	23,656		2.43
Exercisable at March 31, 2013	16,128		$	2.66

Schedule of Share-based Compensation, Restricted Stock Units Award Activity [Table Text Block]

	Shares		Weighted Average Grant Date Fair Value
	(in thousands)
Outstanding at December 31, 2012	3,543		$	1.80
Granted	1,969		2.09
Vested	(991	)	1.80
Forfeited	(37	)	1.85
Nonvested at March 31, 2013	4,484		$	1.93

Schedule of Share-based Compnesation, Performance-based Restricted Stock Units [Table Text Block]

	Shares		Weighted Average Grant Date Fair Value
	(in thousands)
Outstanding at December 31, 2012	329		$	1.90
Vested	(329	)	1.90
Nonvested at March 31, 2013	—		$	—

Schedule of Share-based Payment Award, Stock Options, Valuation Assumptions [Table Text Block]

	Expected Volatility		Risk-free Interest Rate		Expected Term	Dividend Rate
March 31, 2013:
Employees	91	%	0.8	%	5	—	%
Officers and non-employee directors	81	%	1.6	%	8	—	%
March 31, 2012:
Employees	92	%	0.8	%	5	—	%
Officers and non-employee directors	80	%	1.6	%	8	—	%

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Consolidated Statements of Comprehensive Loss (Unaudited) (USD $) In Thousands, except Per Share data, unless otherwise specified	3 Months Ended
	Mar. 31, 2013	Mar. 31, 2012
Revenues:
Collaborative research	$ 284	$ 152
Subscription and license fees	76	148
Total revenues	360	300
Operating expenses:
Research and development, including stock-based compensation of $1,330 and $1,037, respectively	20,327	23,037
Increase in fair value of Symphony Icon, Inc. purchase liability	1,264	2,081
General and administrative, including stock-based compensation of $779 and $681, respectively	4,324	4,565
Total operating expenses	25,915	29,683
Loss from operations	(25,555)	(29,383)
Interest income	53	56
Interest expense	(506)	(537)
Other income (expense), net	34	(4)
Consolidated net loss	(25,974)	(29,868)
Consolidated net loss per common share, basic and diluted	$ (0.05)	$ (0.06)
Shares used in computing consolidated net loss per common share, basic and diluted	512,428	480,324
Unrealized gain (loss) on investments	19	(78)
Comprehensive loss	$ (25,955)	$ (29,946)

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Fair Value Measurements

3 Months Ended

Mar. 31, 2013

Fair Value Measurements [Abstract]

Fair Value, Measurement Inputs, Disclosure

Fair Value Measurements

The Company uses various inputs in determining the fair value of its investments and measures these assets on a recurring basis. Assets and liabilities recorded at fair value in the consolidated balance sheets are categorized by the level of objectivity associated with the inputs used to measure their fair value. The following levels are directly related to the amount of subjectivity associated with the inputs to fair valuation of these assets and liabilities:

• Level 1 - quoted prices in active markets for identical investments

• Level 2 - other significant observable inputs (including quoted prices for similar investments, market corroborated inputs, etc.)

• Level 3 - significant unobservable inputs (including the Company's own assumptions in determining the fair value of investments)

The inputs or methodology used for valuing securities are not necessarily an indication of the credit risk associated with investing in those securities. The following table provides the fair value measurements of applicable Company assets and liabilities that are measured at fair value on a recurring basis according to the fair value levels described above as of March 31, 2013 and December 31, 2012.

	Assets and Liabilities at Fair Value as of March 31, 2013
	Level 1		Level 2		Level 3		Total
	(in thousands)
Assets
Cash and cash equivalents	$	34,248	$	—	$	—	$	34,248
Short-term investments	162,915		—		—		162,915
Total cash and cash equivalents and investments	$	197,163	$	—	$	—	$	197,163
Liabilities
Other long-term liabilities	$	—	$	—	$	31,184	$	31,184
Total liabilities	$	—	$	—	$	31,184	$	31,184

	Assets and Liabilities at Fair Value as of December 31, 2012
	Level 1		Level 2		Level 3		Total
	(in thousands)
Assets
Cash and cash equivalents	$	30,423	$	—	$	—	$	30,423
Short-term investments	192,785		—		—		192,785
Total cash and cash equivalents and investments	$	223,208	$	—	$	—	$	223,208
Liabilities
Other long-term liabilities	$	—	$	—	$	29,920	$	29,920
Total liabilities	$	—	$	—	$	29,920	$	29,920

The Company's Level 3 liabilities are estimated using a probability-based income approach utilizing an appropriate discount rate. Subsequent changes in the fair value of the Symphony Icon purchase consideration liability are recorded as an increase or decrease in Symphony Icon purchase liability expense in the accompanying consolidated statements of comprehensive loss. On July 30, 2012, Lexicon issued 13,237,519 shares of common stock to designees of Symphony Icon Holdings LLC ("Holdings") in satisfaction of the $35 million base payment obligation (see Note 7, Arrangements with Symphony Icon, Inc., for more information). The following table summarizes the change in consolidated balance sheet carrying value associated with Level 3 liabilities for the three months ended March 31, 2013 and 2012.

	Other Long-term Liabilities
	(in thousands)
Balance at December 31, 2012	$	29,920
Change in valuation of purchase consideration payable to former Symphony Icon stockholders	1,264
Balance at March 31, 2013	$	31,184
Balance at December 31, 2011	$	55,033
Change in valuation of purchase consideration payable to former Symphony Icon stockholders	2,081
Balance at March 31, 2012	$	57,114

The Company also has assets that under certain conditions are subject to measurement at fair value on a non-recurring basis. These assets include goodwill associated with the acquisitions of Coelacanth Corporation in 2001 and Symphony Icon on July 30, 2010 and intangible assets associated with the acquisition of Symphony Icon on July 30, 2010. For these assets, measurement at fair value in periods subsequent to their initial recognition is applicable if one or more is determined to be impaired.

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Cash and Cash Equivalents and Investments

3 Months Ended

Mar. 31, 2013

Cash and Cash Equivalents and Investments [Abstract]

Cash and Cash Equivalents Disclosure

Cash and Cash Equivalents and Investments

The fair value of cash and cash equivalents and investments held at March 31, 2013 and December 31, 2012 are as follows:

	As of March 31, 2013
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value
	(in thousands)
Cash and cash equivalents	$	34,248	$	—	$	—		$	34,248
Securities maturing within one year:
Certificates of deposit	550		—		—			550
U.S. treasury securities	162,323		42		—			162,365
Total short-term investments	$	162,873	$	42	$	—		$	162,915
Total cash and cash equivalents and investments	$	197,121	$	42	$	—		$	197,163
	As of December 31, 2012
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value
			(in thousands)
Cash and cash equivalents	$	30,423	$	—	$	—		$	30,423
Securities maturing within one year:
Certificates of deposit	551		—		—			551
U.S. treasury securities	192,211		24		(1		)	192,234
Total short-term investments	$	192,762	$	24	$	(1	)	$	192,785
Total cash and cash equivalents and investments	$	223,185	$	24	$	(1	)	$	223,208

There were no realized gains or losses for the three months ended March 31, 2013, and no realized gains or losses for the three months ended March 31, 2012. The cost of securities sold is based on the specific identification method.

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Stock-Based Compensation (Details 3) (Stock Options [Member], USD $) In Thousands, except Per Share data, unless otherwise specified	3 Months Ended
	Mar. 31, 2013
Stock Options [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock options outstanding	21,525
Stock options outstanding, weighted-average exercise price	$ 2.51
Stock options granted	2,971
Stock options granted, weighted-average exercise price	$ 2.11
Stock options exercised	(140)
Stock options exercised, weighted-average exercise price	$ 1.78
Stock options expired	(695)
Stock options expired, weighted-average exercise price	$ 3.62
Stock options forfeited	(5)
Stock options forfeited, weighted-average exercise price	$ 1.94
Stock options outstanding	23,656
Stock options outstanding, weighted-average exercise price	$ 2.43
Stock options exercisable	16,128
Stock options exercisable, weighted-average exercise price	$ 2.66

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Cash and Cash Equivalents and Investments (Tables)

3 Months Ended

Mar. 31, 2013

Cash and Cash Equivalents and Investments [Abstract]

Schedule of Cash, Cash Equivalents and Short-term Investments [Table Text Block]

	As of March 31, 2013
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value
	(in thousands)
Cash and cash equivalents	$	34,248	$	—	$	—		$	34,248
Securities maturing within one year:
Certificates of deposit	550		—		—			550
U.S. treasury securities	162,323		42		—			162,365
Total short-term investments	$	162,873	$	42	$	—		$	162,915
Total cash and cash equivalents and investments	$	197,121	$	42	$	—		$	197,163
	As of December 31, 2012
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value
			(in thousands)
Cash and cash equivalents	$	30,423	$	—	$	—		$	30,423
Securities maturing within one year:
Certificates of deposit	551		—		—			551
U.S. treasury securities	192,211		24		(1		)	192,234
Total short-term investments	$	192,762	$	24	$	(1	)	$	192,785
Total cash and cash equivalents and investments	$	223,185	$	24	$	(1	)	$	223,208

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Commitments and Contingencies

3 Months Ended

Mar. 31, 2013

Commitments and Contingencies [Abstract]

Commitments and Contingencies Disclosure

Commitments and Contingencies

Operating Lease Obligations:  A Lexicon subsidiary leases laboratory and office space in Hopewell, New Jersey under an agreement which expires in June 2018.  Rent expense is recognized on a straight-line basis over the lease term.  Lexicon is the guarantor of the obligations of its subsidiary under this lease.  The maximum potential amount of future payments the Company could be required to make under this agreement is $5.3 million as of March 31, 2013. The Company is required to maintain restricted investments to collateralize a standby letter of credit for this lease.  The Company had $0.4 million and $0.4 million in restricted investments as collateral as of March 31, 2013 and December 31, 2012, respectively.  Additionally, Lexicon leases certain equipment under operating leases.

Legal Proceedings.  Lexicon is from time to time party to claims and legal proceedings that arise in the normal course of its business and that it believes will not have, individually or in the aggregate, a material adverse effect on its results of operations, financial condition or liquidity.

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Debt Obligations

3 Months Ended

Mar. 31, 2013

Debt Obligations [Abstract]

Debt Disclosure

Debt Obligations

Mortgage Loan.  In April 2004, Lexicon obtained a $34.0 million mortgage on its facilities in The Woodlands, Texas.  The mortgage loan has a ten-year term with a 20-year amortization and bears interest at a fixed rate of 8.23%.  The mortgage had a principal balance outstanding of $23.1 million as of March 31, 2013. The fair value of Lexicon’s mortgage loan approximates its carrying value.  The fair value of Lexicon’s mortgage loan is estimated using discounted cash flow analysis, based on the Company’s current incremental borrowing rate.

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Arrangements with Symphony Icon Inc

3 Months Ended

Mar. 31, 2013

Arrangements with Symphony Icon Inc [Abstract]

Arrangements with Symphony Icon Inc

Arrangements with Symphony Icon, Inc.

On June 15, 2007, Lexicon entered into a series of related agreements providing for the financing of the clinical development of certain of its drug candidates, including LX1032 and LX1033, along with any other pharmaceutical compositions modulating the same targets as those drug candidates (the “Programs”). The agreements included a Novated and Restated Technology License Agreement pursuant to which the Company licensed to Symphony Icon, a then wholly-owned subsidiary of Holdings, the Company's intellectual property rights related to the Programs. Holdings contributed $45 million to Symphony Icon in order to fund the clinical development of the Programs.

Under a Share Purchase Agreement, dated June 15, 2007, between the Company and Holdings, the Company issued and sold to Holdings 7,650,622 shares of its common stock on June 15, 2007 in exchange for $15 million and an exclusive purchase option (the "Purchase Option") that gave the Company the right to acquire all of the equity of Symphony Icon, thereby allowing the Company to reacquire all of the Programs. On July 30, 2010, Lexicon entered into an Amended and Restated Purchase Option Agreement with Symphony Icon and Holdings and simultaneously exercised the Purchase Option, thereby reacquiring the Programs. Pursuant to the amended terms of the Purchase Option, Lexicon paid Holdings $10 million on July 30, 2010 and issued 13,237,519 shares of common stock to designees of Holdings on July 30, 2012 in satisfaction of an additional $35 million base payment obligation.

Lexicon also agreed to make up to $45 million in additional contingent payments, which will consist of 50% of any consideration Lexicon receives pursuant to any licensing transaction (a “Licensing Transaction”) under which Lexicon grants a third party rights to commercialize LX1032, LX1033 or other pharmaceutical compositions modulating the same target as those drug candidates (the “LG103 Programs”), subject to certain exceptions. The contingent payments will be due if and when Lexicon receives such consideration from a Licensing Transaction. In the event Lexicon receives regulatory approval in the United States for the marketing and sale of any product resulting from the LG103 Programs prior to entering into a Licensing Transaction for the commercialization of such product in the United States, in lieu of any contingent payment from such a Licensing Transaction, Lexicon will pay Holdings the sum of $15 million and the amount of certain expenses Lexicon incurred after its exercise of the Purchase Option which are attributable to the development of such product, reduced by up to 50% of such sum for the amount of any contingent payments paid prior to such United States regulatory approval attributable to any such Licensing Transaction outside of the United States with respect to such product. In the event Lexicon makes any such payment upon United States regulatory approval, Lexicon will have no obligation to make subsequent contingent payments attributable to any such Licensing Transactions for the commercialization of such product outside the United States until the proceeds of such Licensing Transactions exceed 50% of the payment made as a result of such United States regulatory approval. The contingent payments may be paid in cash or a combination of cash and common stock, in Lexicon's discretion, provided that no more than 50% of any contingent payment will be paid in common stock.

Lexicon accounted for the exercise of the Purchase Option and acquisition of Symphony Icon as a business combination. In connection with its acquisition of Symphony Icon, Lexicon paid $10.0 million in cash, and also agreed to pay Holdings additional base and contingent payments as discussed above. The fair value of the base and contingent consideration payments was $45.6 million at the date of acquisition and was estimated by applying a probability-based income approach utilizing an appropriate discount rate. This estimation was based on significant inputs that are not observable in the market, referred to as Level 3 inputs. Key assumptions include: (1) a discount rate of 14% for the base payments; (2) a discount rate of 18% for the contingent payments; and (3) a probability adjusted contingency. The discount rate assumptions have not changed through March 31, 2013, and as programs progress, the probability adjusted contingency is adjusted as necessary. Subsequent changes in the fair value of the Symphony Icon purchase consideration liability are recorded as an increase or decrease in fair value of Symphony Icon purchase liability expense in the accompanying consolidated statements of comprehensive loss. During the three months ended March 31, 2013 and 2012, the fair value of the Symphony Icon purchase consideration liability increased by $1.3 million and $2.1 million, respectively.

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Collaboration and License Agreements

3 Months Ended

Mar. 31, 2013

Collaboration and License Agreements [Abstract]

Collaborative Arrangement Disclosure

Collaboration and License Agreements

Lexicon has derived substantially all of its revenues from drug discovery and development collaborations, target validation collaborations for the development and, in some cases, analysis of the physiological effects of genes altered in knockout mice, government grants and contracts, technology licenses, subscriptions to its databases and compound library sales. Revenues generated from third parties under collaborative arrangements are recorded on a gross basis on the consolidated statements of comprehensive loss as Lexicon is the principal participant for these transactions for the purpose of accounting for these arrangements.

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Stock-Based Compensation (Details 1) (USD $) In Millions, unless otherwise specified	3 Months Ended
	Mar. 31, 2013	Mar. 31, 2012
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Allocated Share-based Compensation Expense	$ 2.1	$ 1.7

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Cash and Cash Equivalents and Investments (Details) (USD $) In Thousands, unless otherwise specified	Mar. 31, 2013	Dec. 31, 2012
Cash and Cash Equivalents
Fair Value
Amortized Cost	$ 34,248	$ 30,423
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Estimated Fair Value	34,248	30,423
Certificates of Deposit
Fair Value
Amortized Cost	550	551
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Estimated Fair Value	550	551
U.S. Treasury Securities
Fair Value
Amortized Cost	162,323	192,211
Gross Unrealized Gains	42	24
Gross Unrealized Losses	0	(1)
Estimated Fair Value	162,365	192,234
Total Short-term Investments
Fair Value
Amortized Cost	162,873	192,762
Gross Unrealized Gains	42	24
Gross Unrealized Losses	0	(1)
Estimated Fair Value	162,915	192,785
Total Cash and Cash Equivalents and Investments
Fair Value
Amortized Cost	197,121	223,185
Gross Unrealized Gains	42	24
Gross Unrealized Losses	0	(1)
Estimated Fair Value	$ 197,163	$ 223,208

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Statements of Comprehensive Loss Parenthetical (Parenthetical) (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Mar. 31, 2013	Mar. 31, 2012
Stock-based compensation expense associated with research and development expense	$ 1,330	$ 1,037
Stock-based compensation expense associated with general and administrative expense	$ 779	$ 681

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Stock-Based Compensation

3 Months Ended

Mar. 31, 2013

Stock-Based Compensation [Abstract]

Disclosure of Share-based Compensation Arrangements by Share-based Payment Award

 Stock-Based Compensation

The Company recorded $2.1 million and $1.7 million of stock-based compensation expense for the three months ended March 31, 2013 and 2012, respectively.  The Company utilized the Black-Scholes valuation model for estimating the fair value of the stock compensation granted, with the following weighted-average assumptions for options granted in the three months ended March 31, 2013 and 2012:

	Expected Volatility		Risk-free Interest Rate		Expected Term	Dividend Rate
March 31, 2013:
Employees	91	%	0.8	%	5	—	%
Officers and non-employee directors	81	%	1.6	%	8	—	%
March 31, 2012:
Employees	92	%	0.8	%	5	—	%
Officers and non-employee directors	80	%	1.6	%	8	—	%

The following is a summary of option activity under Lexicon’s stock-based compensation for the three months ended March 31, 2013:

	Options		Weighted Average Exercise Price
	(in thousands)
Outstanding at December 31, 2012	21,525		$	2.51
Granted	2,971		2.11
Exercised	(140	)	1.78
Expired	(695	)	3.62
Forfeited	(5	)	1.94
Outstanding at March 31, 2013	23,656		2.43
Exercisable at March 31, 2013	16,128		$	2.66

During the three months ended March 31, 2013, Lexicon also granted its employees annual restricted stock units. These restricted stock units vest in four annual installments. The following is a summary of restricted stock units activity under Lexicon’s stock-based compensation plans for the three months ended March 31, 2013:

	Shares		Weighted Average Grant Date Fair Value
	(in thousands)
Outstanding at December 31, 2012	3,543		$	1.80
Granted	1,969		2.09
Vested	(991	)	1.80
Forfeited	(37	)	1.85
Nonvested at March 31, 2013	4,484		$	1.93

During 2010, Lexicon granted certain employees restricted stock units with a performance condition. The shares subject to the restricted stock units granted in 2010 vested upon the dosing of the first patient in a pivotal human clinical trial in any country, the results of which could be used to establish safety and efficacy of a pharmaceutical product discovered or developed by Lexicon as a basis for a New Drug Application. This performance condition occurred during the three months ended March 31, 2013, and therefore all outstanding restricted stock units with this performance condition vested. Stock-based compensation expense for awards with performance conditions is recognized over the period from the date the performance condition is determined to be probable of occurring through the time the applicable condition is met. The following is a summary of performance-based restricted stock units activity under Lexicon's stock-based compensation plans for the three months ended March 31, 2013:

	Shares		Weighted Average Grant Date Fair Value
	(in thousands)
Outstanding at December 31, 2012	329		$	1.90
Vested	(329	)	1.90
Nonvested at March 31, 2013	—		$	—

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Cash and Cash Equivalents and Investments (Details 2) (USD $)	3 Months Ended
	Mar. 31, 2013	Mar. 31, 2012
Schedule of Investments [Line Items]
Realized Investment Gains (Losses)	$ 0	$ 0

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Fair Value Measurements (Tables)

3 Months Ended

Mar. 31, 2013

Fair Value Measurements [Abstract]

Fair Value, by Balance Sheet Grouping [Table Text Block]

	Assets and Liabilities at Fair Value as of March 31, 2013
	Level 1		Level 2		Level 3		Total
	(in thousands)
Assets
Cash and cash equivalents	$	34,248	$	—	$	—	$	34,248
Short-term investments	162,915		—		—		162,915
Total cash and cash equivalents and investments	$	197,163	$	—	$	—	$	197,163
Liabilities
Other long-term liabilities	$	—	$	—	$	31,184	$	31,184
Total liabilities	$	—	$	—	$	31,184	$	31,184

	Assets and Liabilities at Fair Value as of December 31, 2012
	Level 1		Level 2		Level 3		Total
	(in thousands)
Assets
Cash and cash equivalents	$	30,423	$	—	$	—	$	30,423
Short-term investments	192,785		—		—		192,785
Total cash and cash equivalents and investments	$	223,208	$	—	$	—	$	223,208
Liabilities
Other long-term liabilities	$	—	$	—	$	29,920	$	29,920
Total liabilities	$	—	$	—	$	29,920	$	29,920

Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation [Table Text Block]

	Other Long-term Liabilities
	(in thousands)
Balance at December 31, 2012	$	29,920
Change in valuation of purchase consideration payable to former Symphony Icon stockholders	1,264
Balance at March 31, 2013	$	31,184
Balance at December 31, 2011	$	55,033
Change in valuation of purchase consideration payable to former Symphony Icon stockholders	2,081
Balance at March 31, 2012	$	57,114