QuickLinks -- Click here to rapidly navigate through this document

UNITED STATES
SECURITIES AND EXCHANGE COMMISSION
WASHINGTON, D.C. 20549

FORM 10-Q/A

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

For The Quarterly Period Ended September 30, 2003

Commission File Number 000-50439

NitroMed, Inc.
(Exact Name of Registrant as Specified in Its Charter)

Delaware (State or Other Jurisdiction of Incorporation or Organization)	22-3159793 (I.R.S. Employer Identification No.)
12 Oak Park Drive, Bedford, Massachusetts (Address of Principal Executive Offices)	01730 (Zip Code)

Registrant's telephone number, including area code: (781) 685-9700

        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 o    No ý

        Indicate by check mark whether the registrant is an accelerated filer (as defined in Rule 12b-2 of the Exchange Act). Yes o    No ý

        As of December 12, 2003, the registrant had 25,578,323 shares of Common Stock, $0.01 par value per share, outstanding.

        This Quarterly Report on Form 10-Q/A amends Part I, Item 1 "Unaudited Financial Statements" to the Registrant's Quarterly Report on Form 10-Q for the quarterly period ended September 30, 2003. The changes are intended to correct certain errors relating to the calculation of net loss per share set forth in the Statements of Operations and Notes 3 and 5 of the Notes to Unaudited Financial Statements in the Quarterly Report on Form 10-Q as previously filed. The changes include the addition of a new Note 1, the reordering of prior Notes 1 through 8 to Notes 2 through 9, the aforesaid corrections to prior Notes 3 and 5 (now Notes 4 and 6) and the inclusion of a new line item, "Deemed dividends related to beneficial conversion features of redeemable convertible preferred stock" in the Statements of Operations and Note 6 of the Notes to Unaudited Financial Statements. In addition, pursuant to the rules of the Securities and Exchange Commission, the Registrant is including in this Form 10-Q/A certain currently dated certifications pursuant to Rules 13a-14(a) and 15d-14 of the Securities Exchange Act of 1934 and 18 U.S.C. Section 1350. Except as previously described, no other changes to the Form 10-Q have been set forth herein.

NITROMED, INC.

FORM 10-Q FOR THE QUARTERLY PERIOD ENDED SEPTEMBER 30, 2003

TABLE OF CONTENTS

		Page Number
Part I.	FINANCIAL INFORMATION	1
Item 1.	Unaudited Financial Statements	1
	Balance Sheets as of September 30, 2003 (unaudited) and December 31, 2002	1
	Statements of Operations for the three and nine months ended September 30, 2003 and 2002 (unaudited)	2
	Statements of Cash Flows for the nine months ended September 30, 2003 and 2002 (unaudited)	3
	Notes to Unaudited Financial Statements	4
Part II.	OTHER INFORMATION	10
Item 6.	Exhibits and Reports on Form 8-K	10
Signatures		11
Exhibit Index		12

ii

PART I. Financial Information

Item 1. Unaudited Financial Statements

NITROMED, INC.

BALANCE SHEETS

(in thousands, except par value amounts)

			September 30, 2003			December 31, 2002
			(unaudited)
Assets
Current assets:
	Cash and cash equivalents		$	7,882		$	5,160
	Marketable securities			26,144			6,683
	Accounts receivable			46			10,000
	Prepaid expenses and other current assets			678			267
Total current assets				34,750			22,110
Property and equipment, net				401			282
Other assets				1,017			100
Total assets			$	36,168		$	22,492
Liabilities and Stockholders' Deficit
Current liabilities:
	Notes payable		$	33		$	42
	Accounts payable			442			695
	Accrued expenses			2,187			1,577
	Deferred revenue			6,377			3,958
Total current liabilities				9,039			6,272
Deferred revenue, long-term				6,667			6,667
Notes payable, less current portion				—			22
Commitments and contingencies
		Redeemable convertible preferred stock, $.01 par value; 34,688 shares authorized at September 30, 2003, and 31,912 shares authorized at December 31, 2002; 33,546 and 30,770 shares issued and outstanding at September 30, 2003 and December 31, 2002, respectively (liquidation value of $105,230)		105,114			82,884
Stockholders' deficit:
		Common stock, $.01 par value; 35,000 shares authorized at September 30, 2003 and 18,077 shares authorized at December 31, 2002; 1,039 shares issued and outstanding at September 30, 2003 and 985 shares issued and outstanding at December 31, 2002		10			10
	Additional paid-in capital			15,184			3,090
	Deferred stock compensation			(3,486	)		(527	)
		Accumulated deficit		(96,360	)		(75,926	)
Total stockholders' deficit				(84,652	)		(73,353	)
Total liabilities and stockholders' deficit			$	36,168		$	22,492

See accompanying notes.

1

NITROMED, INC.

STATEMENTS OF OPERATIONS

(in thousands, except per share amounts) (unaudited)

		Three Months Ended September 30,						Nine Months Ended September 30,
		2003			2002			2003			2002
		(as restated)						(as restated)
Revenues:
	Research and development	$	2,194		$	187		$	5,582		$	562
Operating expenses:
	Research and development		5,041			5,268			13,718			11,868
	General and administrative		651			680			1,903			2,005
Total operating expenses			5,692			5,948			15,621			13,873
Loss from operations			(3,498	)		(5,761	)		(10,039	)		(13,311	)
Non operating income (expense):
	Interest expense		(1	)		(2	)		(3	)		(9	)
	Interest income		88			87			212			324
	Rental income		—			49			82			147
			87			134			291			462
Net loss			(3,411	)		(5,627	)		(9,748	)		(12,849	)
Deemed dividends related to beneficial conversion features of redeemable convertible preferred stock			(8,356	)		—			(8,356	)		—
Dividends and accretion to redemption value of redeemable convertible preferred stock			(981	)		(674	)		(2,330	)		(2,023	)
Net loss attributable to common stockholders		$	(12,748	)	$	(6,301	)	$	(20,434	)	$	(14,872	)
Basic and diluted net loss attributable to common stockholders per common share		$	(12.65	)	$	(6.49	)	$	(20.58	)	$	(15.41	)
Shares used in computing basic and diluted net loss attributable to common stockholders per common share			1,008			971			993			965
Pro forma basic and diluted net loss attributable to common stockholders per common share		$	(0.20	)	$	(0.38	)	$	(0.62	)	$	(0.86	)
Shares used in computing pro forma basic and diluted net loss attributable to common stockholders per common share			16,850			15,001			15,634			14,996

See accompanying notes.

2

NITROMED, INC.

STATEMENTS OF CASH FLOWS

(in thousands)
(unaudited)

			Nine Months Ended September 30,
			2003			2002
Operating activities
Net loss			$	(9,748	)	$	(12,849	)
Adjustments to reconcile net loss to net cash provided by (used in) operating activities:
	Depreciation and amortization			179			172
	Forgiveness of note receivable from stock purchase agreement			—			252
	Stock compensation expense			741			612
	Changes in operating assets and liabilities:
		Accounts receivable		9,954			64
		Prepaid expenses and other assets		(1,328	)		337
		Deferred revenue		2,419			(562	)
		Accounts payable and accrued expenses		357			(297	)
Net cash provided by (used in) operating activities				2,574			(12,271	)
Investing activities
Purchases of property and equipment				(300	)		(39	)
Net purchases of marketable securities				(19,461	)		(135	)
Net cash used in investing activities				(19,761	)		(174	)
Financing activities
Principal payments on notes payable				(31	)		(279	)
Proceeds from exercise of stock options				40			25
Net proceeds from sale of redeemable convertible preferred stock				19,900			—
Net cash provided by (used in) financing activities				19,909			(254	)
Net increase (decrease) increase in cash and cash equivalents				2,722			(12,699	)
Cash and cash equivalents at beginning of period				5,160			20,672
Cash and cash equivalents at end of period			$	7,882		$	7,973

See accompanying notes.

3

NITROMED, INC.
NOTES TO UNAUDITED FINANCIAL STATEMENTS

September 20, 2003

(1) Restatement of Quarterly Financial Statements

        The Company is restating its net loss attributable to common stockholders and net loss attributable to common stockholders per common share for the three and nine month periods ended September 30, 2003 because the deemed dividends related to the beneficial conversion features for Series E and Series F, which are disclosed in Note 7, were inadvertently excluded from the calculations of net loss attributable to common stockholders and net loss attributable to common stockholders per common share.

        A summary of the significant effects of the revision are as follows (in thousands, except per share amount):

	Three months ended September 31, 2003			Nine months ended September 31, 2003
Net loss attributable to common stockholders as previously reported	$	(4,392	)	$	(12,078	)
Net loss attributable to common stockholders as restated	$	(12,748	)	$	(20,434	)
Basic and diluted net loss attributable to common stockholders per common share as previously reported	$	(4.36	)	$	(12.16	)
Basic and diluted net loss attributable to common stockholders per common share as restated	$	(12.65	)	$	(20.58	)

(2) Basis of Presentation

        The accompanying unaudited financial statements of NitroMed, Inc. ("NitroMed" or the "Company") have been prepared in accordance with accounting principles generally accepted in the United States (GAAP) for interim financial information and with the instructions to Form 10-Q and Article 10 of Regulation S-X. Accordingly, they do not include all of the information and footnotes required by GAAP for complete financial statements. In the opinion of management, all adjustments (consisting of normal recurring accruals) considered necessary for the fair presentation of the results for the interim periods have been included. The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the amounts reported in the financial statements and accompanying notes. Interim results are not necessarily indicative of results to be expected for the entire fiscal year ended December 31, 2003. These unaudited financial statements should be read in conjunction with the audited financial statements and related notes thereto included in the Company's latest audited annual financial statements. Those audited financial statements are included in the Company's Registration Statement on Form S-1 (No. 333-108104), which has been filed with the Securities and Exchange Commission (SEC).

        The preparation of financial statements in conformity with accounting principles generally accepted in the United States requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the financial statements and the reported amounts of revenue and expenses during the reporting period. Actual results could differ from those estimates.

4

(3) Subsequent Events

Initial Public Offering

        On November 10, 2003, the Company completed an initial public offering which, after deducting underwriting discounts and expenses and estimated offering-related expenses, resulting in net proceeds to the Company of approximately $60.1 million and issuance by the Company of 6,000,000 shares of common stock at $11.00 per share. In connection with the initial public offering, all of the outstanding shares of the Company's redeemable convertible preferred stock, including accrued but unpaid dividends, were converted into 18,398,496 shares of the Company's common stock. Because the offering closed after September 30, 2003, the results of the offering are not reflected in the accompanying unaudited financial statements. A summary of the terms of this offering can be found in the Company's Registration Statement on Form S-1 (No. 333-108104), which has been filed with the SEC.

Merck Agreement

        On December 3, 2003, the Company received the second milestone payment of $5.0 million from Merck for advancing a lead nitric oxide enhancing COX-2 inhibitor into human testing.

Lease Agreement

        On November 10, 2003, the Company entered into a non-binding letter of intent to lease approximately 52,000 square feet of office and laboratory space in Lexington, Massachusetts. The lease, if entered into, would increase the Company's annual lease commitments over the next five years. Because the Company has not yet reached a definitive agreement, it is not currently able to estimate the expected increase. The lease is expected to have a term of ten years, subject to renewal, commencing on or about August 1, 2004.

(4) Stock-Based Compensation

        The Company has elected to account for its stock-based compensation plans following Accounting Principles Board Opinion No. 25, Accounting for Stock Issued to Employees (APB 25), and related Interpretations, rather than the alternative fair value accounting provided under Statement of Financial Accounting Standards No. 123, Accounting for Stock-Based Compensation (FAS 123). In accordance with EITF 96-18, Accounting for Equity Instruments that are Issued to Other than Employees for Acquiring, or in Connection with Selling Goods or Services (EITF 96-18), the Company records compensation expense equal to the fair value of the option granted to non-employees over the vesting period, which is generally the period of service.

        For the nine month period ended September 30, 2003 and the year ended December 31, 2002, the Company granted 413,250 and 241,000 options, respectively, to employees at exercise prices below the fair value of the Company's common stock. The Company has recorded deferred stock compensation expense related to these grants of $3,317,000 and $566,000 for the nine month period ended September 30, 2003 and year ended December 31, 2002, respectively. These amounts are being recognized ratably over the vesting period of four years. Included in the results of operations for the nine month periods ended September 30, 2003 and 2002 is compensation expense of $361,000 and $17,000, respectively.

5

        For purposes of pro forma disclosures, the estimated fair value of the options is amortized over the options vesting period. Had compensation expense for the Company's stock-based compensation plans been determined based on the fair value at the grant dates for awards under those plans consistent with the method of FAS 123, the Company's net loss would have been as follows:

		Three Months Ended September 30,						Nine Months Ended September 30,
		2003			2002			2003			2002
Net loss attributable to common stockholders as reported		$	(12,748	)	$	(6,301	)	$	(20,434	)	$	(14,872	)
Add: Stock-based employee compensation expense included in reported net loss			259			30			522			477
Deduct: Stock-based employee compensation expense determined under fair value based method			(569	)		(76	)		(886	)		(222	)
	Pro forma net loss	$	(13,058	)	$	(6,347	)	$	(20,798	)	$	(14,617	)
Basic and diluted net loss per share
	As reported	$	(12.65	)	$	(6.49	)	$	(20.58	)	$	(15.41	)
	Pro forma	$	(12.95	)	$	(6.54	)	$	(20.94	)	$	(15.15	)

(5) Comprehensive Income (Loss)

        Components of comprehensive income (loss) include net income (loss) and certain transactions that have generally been reported in the statement of stockholders' equity. Other comprehensive loss is the same as the net loss for all periods presented.

(6) Net Loss Per Share and Pro Forma Net Loss Per Share

        Basic net loss per share is computed by dividing net loss available to common stockholders by the weighted average number of shares of common stock outstanding during the period. Diluted net loss per share is computed by dividing net loss available to common stockholders by the weighted average number of shares of common stock and the dilutive potential common stock equivalents then outstanding. Potential common stock equivalents consist of stock options, warrants and redeemable convertible preferred stock. Since the Company has a net loss for all periods presented, the effect of all potentially dilutive securities is antidilutive. Accordingly, basic and diluted net loss per share is the same.

        Pro forma net loss per share is computed using the weighted average number of common shares outstanding, including the pro forma effects of the automatic conversion of all outstanding redeemable convertible preferred stock, into shares of the Company's common stock effective upon the assumed closing of the Company's initial public offering, as if such conversion had occurred at the date of the original issuance.

        The following table sets forth the computation of basic and diluted net loss per share and pro forma basic and diluted net loss per share for the respective periods. The pro forma basic and diluted

6

net loss per share gives effect to the conversion of the redeemable convertible preferred stock as if converted at the date of original issuance.

	Three Months Ended September 30,						Nine Months Ended September 30,
	2003			2002			2003			2002
Basic and Diluted:
Net loss	$	(3,411	)	$	(5,627	)	$	(9,748	)	$	(12,849	)
Deemed dividends related to beneficial conversion features of redeemable convertible preferred stock		(8,356	)		—			(8,356	)		—
Dividends and accretion to redemption value of redeemable convertible preferred stock		(981	)		(674	)		(2,330	)		(2,023	)
Net loss attributable to common stockholders	$	(12,748	)	$	(6,301	)	$	(20,434	)	$	(14,872	)
Weighted average common shares used to compute net loss per share		1,008			971			993			965
Basic and diluted net loss per share	$	(12.65	)	$	(6.49	)	$	(20.58	)	$	(15.41	)
Pro forma basic and diluted:
Net loss	$	(3,411	)	$	(5,627	)	$	(9,748	)	$	(12,849	)
Weighted average common shares used to compute net loss per share		1,008			971			993			965
Weighted average number of common shares assuming the conversion of all redeemable convertible preferred stock at the original date of issuance		15,842			14,030			14,641			14,031
Weighted average common shares used to compute pro forma net loss per share		16,850			15,001			15,634			14,996
Pro forma basic and diluted net loss per share	$	(0.20	)	$	(0.38	)	$	(0.62	)	$	(0.86	)

(7) Redeemable Convertible Preferred Stock and Stockholders' Deficit

        In March 2003 the Company's Board of Directors adopted, and in May 2003, the Company's stockholders approved, the 2003 Stock Incentive Plan, under which 800,000 shares of common stock were authorized for issuance. On August 18, 2003, the Board of Directors approved and in October 2003, the stockholders approved, an increase of shares authorized for issuance under the plan to 2,500,000. On August 18, 2003, the Board of Directors adopted the 2003 Employee Stock Purchase Plan, which provides for the sale of up to 75,000 shares of common stock to participating employees.

        On August 1, 2003, the Company completed the sale of 2,776,347 shares of series E redeemable convertible preferred stock for net proceeds of $19.9 million. These shares automatically converted to common stock upon the closing of the Company's initial public offering of common stock on November 10, 2003, which was subsequent to the end of the Company's third fiscal quarter reported on herein. These shares contained a beneficial conversion feature based on the fair value of the common

7

stock into which the shares were convertible. In accordance with EITF 98-5, "Accounting for Convertible Securities with Beneficial Conversion Features or Contingently Adjustable Conversion Ratios," the value of such beneficial conversion feature of approximately $8.3 million has been recognized as a deemed dividend in the three month period ended September 30, 2003. As a result of the sale of these Series E shares, the Series F conversion ratio was increased from 1:1 to 1:1.073364. The adjustment to the Series F conversion ratio is a beneficial conversion feature. In accordance with EITF 00-27, "Application of Issue 98-5 to Certain Convertible Instruments," the value of such beneficial conversion feature of approximately $37,000 has been recognized as a deemed dividend in the three month period ended September 30, 2003.

        Subsequent to the August 2003 sale of the Series E, the Series E stockholders and the Company agreed to increase the Series E conversion ratio from 1:1 to 1:1.1526 in consideration of the Series E stockholders waiving their rights to certain anti-dilution provisions. The adjustment to the conversion ratio, which was contingent on the initial public offering, is a beneficial conversion feature. In accordance with EITF 00-27, the value of the Series E beneficial conversion feature of approximately $11.0 million will be recognized as a deemed dividend in the period of issuance, which occurred in the fourth quarter of 2003 as a result of the initial public offering. In addition, the conversion of the Series E shares in the initial public offering subsequent to the end of the third fiscal quarter caused the accrued but unpaid Series E dividends of approximately $6.4 million to become payable through the issuance of 513,033 shares of common stock at the time of the initial public offering.

        On August 18 2003, the Board of Directors approved an Amendment to Certificate of Incorporation, which became effective on November 5, 2003 and increased the Company's authorized shares of common stock to 35,000,000. On August 18, 2003, the Board of Directors also approved a Restated Certificate of Incorporation, which became effective upon the consummation of the initial public offering on November 10, 2003 and increased the Company's authorized shares of common stock to 65,000,000 and authorized 5,000,000 shares of undesignated preferred stock, issuable in one or more series designated from time to time by the Board of Directors.

        Upon consummation of the initial public offering on November 10, 2003 all outstanding shares of redeemable convertible preferred stock and all accrued but unpaid Series E dividends noted above, were converted into 18,398,496 shares of common stock based upon the conversion ratios then applicable.

(8) Commitments and Contingencies

        An academic institution has asserted that patents and patent applications which relate to the nitric oxide stent program may require a license from such institution. It is the opinion of the Company's management and legal counsel that the disputed intellectual property has been validly licensed to, or is validly owned by, the Company. Accordingly, the accompanying financial statements do not include any provision related to this claim.

(9) New Accounting Pronouncements

        In November 2002, the EITF issued EITF 00-21, "Revenue Arrangements with Multiple Deliverables," (EITF 00-21) which addresses certain aspects of the accounting for arrangements that involve the delivery or performance of multiple products, services and/or rights to use assets. Under

8

EITF 00-21, revenue arrangements with multiple deliverables should be divided into separate accounting units if the deliverables meet certain criteria, including whether the fair value of the delivered items can be determined and whether there is evidence of fair value of the undelivered items. In addition, the consideration should be allocated among the separate units of accounting based on their fair values, and the applicable revenue recognition criteria should be considered separately for each of the separate units of accounting. EITF 00-21 is effective for revenue arrangements entered into after June 30, 2003. The Company has adopted EITF 00-21, which did not have a material impact on its financial position or results of operations.

        In January 2003, the FASB issued Interpretation No. 46, "Consolidation of Variable Interest Entities" (FIN 46), which is an interpretation of Accounting Research Bulletin No. 51, "Consolidated Financial Statements." FIN 46 requires that if an entity has a controlling interest in a variable interest entity, the assets, liabilities and results of activities of the variable interest entity should be included in the consolidated financial statements of the entity. FIN 46 is effective immediately for all new variable interest entities created or acquired after January 31, 2003. For variable interest entities created or acquired prior to February 1, 2003, the provisions of FIN46 must be applied in the first interim or annual period beginning after December 15, 2003. The Company does not expect that the adoption of FIN 46 will have a material effect on its financial position or results of operations.

        In May 2003, the FASB issued SFAS No. 150, "Accounting for Certain Financial Instruments with Characteristics of both Liabilities and Equity." This statement establishes how a company classifies and measures certain financial instruments with characteristics of both liabilities and equity, including redeemable preferred stock. This statement is effective for financial instruments entered into or modified after May 31, 2003, and otherwise effective at the beginning of the interim period commencing July 1, 2003. The adoption of this statement did not have a material impact on the Company's financial position or results of operations.

9

Part II. OTHER INFORMATION

Item 6. Exhibits and Reports on Form 8-K

(a)	Exhibits
	31.1	Certification of the Chief Executive Officer pursuant to Rule 13a-14(a) and 15d-14 of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002
	31.2	Certification of the Chief Financial Officer pursuant to Rule 13a-14(a) and 15d-14 of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002
	32.1	Certification of the Chief Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002
	32.2	Certification of the Chief Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.
(b)	There were no reports on Form 8-K filed or furnished by the Company during the fiscal quarter ended September 30, 2003.

10

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.

	NITROMED, INC.
Date: March 29, 2004	By:	/s/  JOSEPH GRIMM Joseph Grimm Senior Vice President, Business Development and Chief Financial Officer, Treasurer and Secretary (Principal Financial Officer)

11

EXHIBIT INDEX

Exhibit Number	Description
31.1	Certification of the Chief Executive Officer pursuant to Rule 13a-14(a) and 15d-14 of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002
31.2	Certification of the Chief Financial Officer pursuant to Rule 13a-14(a) and 15d-14 of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002
32.1	Certification of the Chief Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002
32.2	Certification of the Chief Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.

12

QuickLinks

TABLE OF CONTENTS

PART I. Financial Information
Item 1. Unaudited Financial Statements

NITROMED, INC. BALANCE SHEETS (in thousands, except par value amounts)
NITROMED, INC. STATEMENTS OF OPERATIONS (in thousands, except per share amounts) (unaudited)
NITROMED, INC. STATEMENTS OF CASH FLOWS (in thousands) (unaudited)
NITROMED, INC. NOTES TO UNAUDITED FINANCIAL STATEMENTS September 20, 2003

Part II. OTHER INFORMATION
Item 6. Exhibits and Reports on Form 8-K

SIGNATURES
EXHIBIT INDEX