UNITED STATES
SECURITIES AND EXCHANGE COMMISSIONWashington, D.C. 20549

---

FORM 10-K/AAMENDMENT NO. 1

FOR ANNUAL AND TRANSITION REPORTS PURSUANT TO
SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

|(Mark One)                                                       |                                                                                         
|---------------------------------------------------------------- | ----------------------------------------------------------------------------------------
|ý                                                                | ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934    
|For the fiscal year ended December 31, 2003                     
|OR                                                              
|o                                                                | 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 000-50439

---

NITROMED, INC.(Exact name of registrant as specified in its charter)

|Delaware(State or other jurisdiction of
incorporation or organization)            |  | 22-3159793(IRS 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) 275-9700

---

Securities registered pursuant to Section 12(b) of the Act:None

Securities registered pursuant to Section 12(g) of the Act:Common Stock, $.01 par value per share
(Title of class)

---

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 ý    NO o

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K is not contained herein, and will not be contained, to the
best of registrant's knowledge, in definitive proxy or information statements incorporated by reference in Part III of this Form 10-K or any amendment to this
Form 10-K. ý

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

The aggregate market value of the registrant's common stock held by nonaffiliates of the registrant as of March 19, 2004 was approximately $82,141,386, based on the price
at which the registrant's common stock was last sold on March 19, 2004. Information regarding the aggregate market value of the registrant's common stock as of June 30, 2003 has not been
provided due to the fact that trading of the registrant's common stock on the Nasdaq National Market did not commence until November 6, 2003.

As
of March 19, 2004, there were 25,600,744 shares of the registrant's common stock outstanding.



---





EXPLANATORY NOTE

This Amendment No. 1 on Form 10-K/A to our Annual Report on Form 10-K for the year ended December 31, 2003
that was originally filed with the Securities and Exchange Commission on March 30, 2004 is being filed to provide additional information required by Items 10, 11, 12, 13 and 14 of
Part III. This Amendment No. 1 on Form 10-K/A does not change our previously reported financial statements and other financial disclosure.

PART III

ITEM 10. DIRECTORS AND EXECUTIVE OFFICERS OF THE REGISTRANT

Directors

Currently, our board of directors is comprised of eight directors. Our directors are elected annually by the stockholders and hold office until the next annual
meeting and until successors are elected and qualified or until death, resignation or removal. Vacancies and newly created directorships resulting from any increase in the authorized number of
directors may be filled until the next annual meeting of stockholders by a majority of directors then in office.

Set
forth below are the names of each member of our board of directors, their ages, the year in which each first became one of our directors, their principal occupations and employment
during the past five years and the names of other public companies of which they serve as a director.

Argeris Karabelas, Ph.D.,age 51, became a director in 2002.

Argeris Karabelas, Ph.D.has served as a member of our board of directors since January 2002 and as our Chairman since
August 2003. Since November 2001, he has been a partner in Care Capital LLC, a life sciences investment firm. From June 2000 to November 2001, Dr. Karabelas served
as Chairman of Novartis BioVentures Ltd., a private equity firm affiliated with Novartis A.G., a pharmaceutical company. Dr. Karabelas has also served as Chief Executive Officer of
Worldwide Pharmaceuticals for Novartis AG from January 1998 to July 2000. He is a member of the Scientific Advisory Council of Massachusetts General Hospital and the Visiting Committee
for Health Sciences and Technology at Massachusetts Institute of Technology. In addition, Dr. Karabelas serves as a director of Halsey Drug Co., Inc., Human Genome Sciences, Inc.
and SkyePharma plc. Dr. Karabelas holds a Ph.D. in pharmacokinetics from the Massachusetts College of Pharmacy.

Michael D. Loberg, Ph.D.,age 56, became a director in 1997.

Michael D. Loberg, Ph.D.has served as a member of our board of directors and as our Chief Executive Officer since September 1997.
He has served as President since September 2003. From 1996 to January 1997, Dr. Loberg served as President of Bristol-Myers Squibb Company's Oncology and Immunology division, a
pharmaceuticals company. From 1994 to 1996, Dr. Loberg served as President of Bristol-Myers Squibb Company's U.S. Primary Care division. Dr. Loberg also serves as a director of Advanced
Magnetics, Inc. Dr. Loberg holds a B.S. in chemistry from Trinity College and a Ph.D. in chemistry from Washington University.

Robert S. Cohen,age 61, became a director in 1997.

Robert S. Cohenhas served as a member of our board of directors since July 1997. Mr. Cohen has served as a consultant to
pharmaceutical and biotechnology companies for the past two years. From October 1999 to May 2001, Mr. Cohen served as Chief Executive Officer of Memory Pharmaceuticals Corp., a
pharmaceutical company. From March 1997 to June 1999, Mr. Cohen served as President and Chief Executive Officer of Shire Laboratories Inc., a drug delivery company.
Mr. Cohen also served first as Chief Operating Officer and then Chief Executive Officer of Pharmavene Inc. which subsequently merged with Shire Pharmaceutical Group, plc.
Mr. Cohen holds a B.S. and an M.S.

1

---



degree
from Brooklyn College of Pharmacy of Long Island University and attended the Harvard Business School Advanced Management Program.

Zola Horovitz, Ph.D.,age 69, became a director in 1997.

Zola P. Horovitz, Ph.D.has served as a member of our board of directors since September 1997. Dr. Horovitz has served as a
consultant to the pharmaceutical and biotechnology industries since 1994. Prior to his retirement in 1994, Dr. Horovitz served as Vice President, Business Development and Planning for
Bristol-Myers Squibb Company. He also serves as a Director of Avigen, Inc., BioCryst Pharmaceuticals, Inc., DOV Pharmaceutical, Inc., Genaera Corporation, GenVec, Inc.,
Paligent Inc. and Palatin Technologies, Inc. Dr. Horovitz holds a Ph.D. in pharmacology from the University of Pittsburgh.

Mark Leschly,age 35, became a director in 1996.

Mark Leschlyhas served as a member of our board of directors since September 1996. Since July 1999, Mr. Leschly has
been a Managing Partner with Rho Capital Partners, an investment and venture capital management company. Starting in July 1994 to July 1999, Mr. Leschly was an associate and then
a General Partner of HealthCare Ventures, L.L.C., a venture capital management company. From September 1991 to June 1993, Mr. Leschly served as a consultant for McKinsey &
Co., a management consulting company. In addition to being a director of Diversa Corporation, a biotechnology company, Mr. Leschly is a director of a number of private companies.
Mr. Leschly holds a B.A. degree from Harvard University and an M.B.A. from the Stanford Graduate School of Business.

John W. Littlechild,age 52, became a director in 1999.

John W. Littlechildhas served as a member of our board of directors since June 1999. Mr. Littlechild previously served as
our President from inception to May 1993 and as a director from May 1992 to December 1997. Since January 1991, he has served as General Partner of HealthCare Ventures,
L.L.C., a venture capital management company. He currently serves on the Executive Committee of the Board of Fellows for Harvard Medical School as well as on the Science and Technology Committee and
as
Chairman of the Microbiology Department Advisory Board. Mr. Littlechild also serves as a director of Dyax Corp. and Orthofix International NV. Mr. Littlechild holds a B.Sc. from the
University of Manchester in England and an M.B.A. from the Manchester Business School.

Joseph Loscalzo, M.D., Ph.D.,age 52, became a director in 2004.

Joseph Loscalzo, M.D., Ph.D.has served as a member of our board of directors since January 2004. Since 1994 he has been a member
of the faculty of Boston University, first as Chief of Cardiology and, since 1997, Chairman of the Department of Medicine. Dr. Loscalzo is also currently the Director of the Whitaker
Cardiovascular Institute at Boston University School of Medicine and Physician-in-Chief at the Boston Medical Center. From 1984 to 1994, Dr. Loscalzo was a member of the
faculty of Harvard University, where he rose to the rank of Associate Professor of Medicine, and of the staff at Brigham and Women's Hospital, where he became the Director of the Center for Research
in Thormbolysis. Dr. Loscalzo holds an A.B., M.D., and a Ph.D. in biochemistry from the University of Pennsylvania.

Davey S. Scoon,age 57, became a director in 2003.

Davey S. Scoonhas served as a member of our board of directors since November 2003. Since October 2003, he has been Chief
Administrative and Financial Officer of Tom's of Maine. He also serves as Non-Executive Chairman of the Board of Directors of Tufts Health Plan, where he has been a director since 1981.
Prior to joining Tom's of Maine, Mr. Scoon served as Chief Administrative and Financial Officer for SunLife Financial from 1999 to 2003. From 1985 to 1999, Mr. Scoon was employed by
Liberty Funds Group of Boston (formerly Colonial Management) as Executive Vice

2

---



President
and Chief Operating Officer. Mr. Scoon holds a B.A. from the University of Wisconsin and an M.B.A. from the Harvard Business School.

Executive Officers

Our executive officers, their respective ages and their positions are as follows:

|Name                     |  | Age |  | Position                                                                                        
|------------------------ |  | --- |  | ------------------------------------------------------------------------------------------------
|Michael D. Loberg, Ph.D. |  | 56  |  | President and Chief Executive Officer and Director                                              
|L. Gordon Letts, Ph.D.   |  | 56  |  | Senior Vice President, Research and Development and Chief Scientific Officer                    
|Joseph Grimm             |  | 53  |  | Senior Vice President, Business Development and Chief Financial Officer, Treasurer and Secretary
|Manuel Worcel, M.D.      |  | 65  |  | Chief Medical Officer                                                                           

Michael D. Loberg, Ph.D., age 56, has served as a member of our board of directors and as our Chief Executive Officer since
September 1997. He has served as President since September 2003. From 1996 to January 1997, Dr. Loberg served as President of Bristol-Myers Squibb Company's Oncology and
Immunology division, a pharmaceuticals company. From 1994 to 1996, Dr. Loberg served as President of Bristol-Myers Squibb Company's U.S. Primary Care division. Dr. Loberg also serves as
a director of Advanced Magnetics, Inc. Dr. Loberg holds a B.S. in chemistry from Trinity College and a Ph.D. in chemistry from Washington University.

L. Gordon Letts, Ph.D., age 56, has served as our Senior Vice President, Research and Development and as our Chief Scientific Officer
since May 1997. From December 1993 to May 1997, Dr. Letts served as our Vice President, Research. From 1987 to 1993, he served as Director of Pharmacology for Boehringer
Ingelheim Pharmaceuticals, a United States subsidiary of a German pharmaceuticals company. Dr. Letts currently serves as a Vice President of the International Association of Inflammation
Societies and serves on the scientific advisory board of IPS Pharma, Inc., a privately-held biopharmaceutical company. Dr. Letts holds a Ph.D. in pharmacology from Sydney
University.

Joseph Grimm, age 53, has served as our Senior Vice President, Business Development, and as our Chief Financial Officer since
April 1999. Mr. Grimm has tendered his resignation as our Senior Vice
President, Business Development and Chief Financial Officer, Treasurer and Secretary, effective as of the earlier of September 1, 2004 or the date when a new Chief Financial Officer begins
employment with us. From October 1997 to January 1999, he served as Chief Financial Officer of Alpha-Beta Technology, Inc., a biopharmaceutical company, and from
May 1986 to April 1997, he served as Vice President Finance and Treasurer of Genetics Institute, Inc., a biopharmaceutical company. Mr. Grimm holds a B.A. from the
University of Wisconsin and a M.B.A. from the University of Minnesota.

Manuel Worcel, M.D., age 65, has served as our Chief Medical Officer since 1997. He also served as our President from
September 1993 to September 2003. From 1993 to 1997, Dr. Worcel also served as our Chief Executive Officer and as a director. From 1989 to 1993, Dr. Worcel served as Head
of Cardiovascular Research and Development of Ciba Geigy Corp., a pharmaceutical company. Dr. Worcel has served as a professor at the Institut de la Sante et de la Recherche Medicale in France
and is currently a Fellow of the Hypertension Council of the American Heart Association. Dr. Worcel holds a M.D. from the University of Buenos Aires.

3

---



Audit Committee

We have a separately-designated standing Audit Committee established in accordance with Section 3(a)(58)(A) of the Exchange Act. The members of our Audit
Committee are Davey S. Scoon, Robert S. Cohen and Zola Horovitz, Ph.D.

Section 16(a) Beneficial Ownership Reporting Compliance

Section 16(a) of the Securities Exchange Act of 1934 requires our directors, executive officers and the holders of more than 10% of our common stock to
file with the SEC initial reports of ownership of our common stock and other equity securities on a Form 3 and reports of changes in such ownership on a Form 4 or Form 5.
Officers, directors and 10% stockholders are required by SEC regulations to furnish us with copies of all Section 16(a) forms they file. Based solely on a review of our records and written
representations by the persons required to file these reports, we believe that all filing requirements of Section 16(a) were satisfied with respect to our most recent fiscal year.

4

---





ITEM 11. EXECUTIVE COMPENSATION

Executive Compensation

The table below sets forth the total compensation paid or accrued for the fiscal years ended December 31, 2003, 2002 and 2001 to our chief executive
officer and each of our three most highly compensated other executive officers who were serving as executive officers on December 31, 2003 and whose total annual compensation exceeded $100,000
for the year ended December 31, 2003. We refer to these officers as our named executive officers.

Summary Compensation Table

|                                                                                                               |  |                |  | Annual Compensation |                         | Long-Term
Compensation
Awards |   |                      
|-------------------------------------------------------------------------------------------------------------- |  | -------------- |  | ------------------- | ----------------------- | ----------------------------- | - | ---------------------
|
|Michael D. Loberg, Ph.D.
President and Chief Executive Officer                                                 |  | 2003
2002
2001 |  | $                   | 319,693
304,560
284,502 |                               | $ | 136,889
90,577
74,682
|Manuel Worcel, M.D.
Chief Medical Officer                                                                      |  | 2003
2002
2001 |  |                     | 259,121
246,774
238,451 |                               |   | 87,588
52,439
44,705 
|L. Gordon Letts, Ph.D.
Senior Vice President, Research and Development and Chief Scientific Officer            |  | 2003
2002
2001 |  |                     | 239,080
227,689
219,989 |                               |   | 77,596
46,750
36,298 
|Joseph Grimm (4)
Senior Vice President, Business Development, Chief Financial Officer, Treasurer and Secretary |  | 2003
2002
2001 |  |                     | 216,243
205,947
198,989 |                               |   | 72,574
38,512
32,825 

---

Option Grants in Last Fiscal Year

The following table sets forth certain information concerning grants of stock options to purchase shares of our common stock made to executive officers named in
the Summary Compensation Table during the fiscal year ended December 31, 2003.

5

---



Option Grants in Last Fiscal Year

|                         |  | Individual Grants |  | Potential Realizable Value at
Assumed Annual Rates of Stock
Price Appreciation
for Option Term (1)
|------------------------ |  | ----------------- |  | --------------------------------------------------------------------------------------------------
|
|
|
|Michael D. Loberg, Ph.D. |  | 100,000
130,000   |  | 10%
13%                                                                                           
|Manuel Worcel, M.D.      |  | 55,000
75,000     |  | 6%
  8%                                                                                           
|L. Gordon Letts, Ph.D.   |  | 55,000
75,000     |  | 6%
  8%                                                                                           
|Joseph Grimm             |  | 35,000
60,000     |  | 4%
  6%                                                                                           

---

Aggregated Option Exercises and Fiscal Year-End Option Value Table

The following table sets forth certain information regarding the exercise of stock options during the fiscal year ended December 31, 2003 and the number
and value of unexercised options held as of December 31, 2003 by the executive officers named in the Summary Compensation Table.

Aggregated Option Exercises in Last Fiscal Year
and Fiscal Year-End Option Values

|                         |  |         |  |         |  | Number of
Securities
Underlying
Unexercised
Options at Fiscal
Year-End (#) |  | Value of
Unexercised
In-The-Money
Options at Fiscal
Year-End ($)(2)
|------------------------ |  | ------- |  | ------- |  | -------------------------------------------------------------------------- |  | -------------------------------------------------------------------
|
|Michael D. Loberg, Ph.D. |  |        |  |        |  | 212,940/272,060                                                            |  | $                                                                  
|Manuel Worcel, M.D.      |  | 30,469  |  | 58,500  |  | 317,345/151,930                                                            |  | $                                                                  
|L. Gordon Letts, Ph.D.   |  | 100,525 |  | 138,672 |  | 182,695/210,430                                                            |  | $                                                                  
|Joseph Grimm             |  |        |  |        |  | 115,965/110,335                                                            |  | $                                                                  

---

6

---



Employment Letters

We have entered into employment letters with the following executive officers: Dr. Loberg, Dr. Worcel and Dr. Letts. Each of these agreements
provide for severance payments in the event of a termination by us without cause up to an amount equal to six months of such executive officer's base salary. In addition, Dr. Worcel's agreement
provides that in the event of a sale of our company prior to July 1 of any calendar year, Dr. Worcel will receive 50% of his scheduled bonus for such year, and if such sale occurs
anytime after July 1 of any calendar year, he will be entitled to 100% of his scheduled bonus for such year.

We
are in the process of negotiating a Severance and Settlement Agreement and Release with Mr. Grimm to set forth the terms that will govern his separation from the company. We
anticipate that Mr. Grimm will remain as Senior Vice President, Business Development and Chief Financial Officer, Treasurer and Secretary until the earlier of September 1, 2004 or the
date when a new Chief Financial Officer is hired. Upon his separation, we currently anticipate that Mr. Grimm will receive six months of his base salary as severance pay and a bonus payment
equal to $3,739.21 per each bi-monthly pay period between January 1, 2004 and his separation date. In addition, for the six-month period after Mr. Grimm's
separation, we anticipate that we will contribute toward the health and dental insurance premiums for Mr. Grimm's coverage. We anticipate that we will accelerate the vesting of
Mr. Grimm's options to purchase 31,418 shares of the company's common stock and will provide Mr. Grimm with twelve months after his separation date in which to exercise
such options. Finally, we anticipate that Mr. Grimm will be available to provide consulting services to us through December 31, 2004 at the rate of $2,500 per day.

Each
executive officer has signed our standard form of invention and non-disclosure agreement, providing for protection of our confidential information and ownership of
intellectual property developed by such executive officer and our standard form of non-competition and non-solicitation agreement, providing for a one-year
non-compete and one year non-solicitation agreement.

Compensation of Directors

Effective August 2003, we compensate our directors for service on the board of directors in the amount of $4,000 per quarter. In addition, members of the
audit committee will receive $2,000 per committee meeting and members of the compensation committee and nominating and corporate governance committee will receive $1,000 per committee meeting. The
chair of the audit committee will receive an additional $2,000 per year, and the chair of the compensation committee and the chair of the nominating and corporate governance committee will each
receive an additional $1,000 per year. Directors are reimbursed for reasonable travel and other expenses incurred in connection with attending meetings of the board of directors and its committees.

Directors
are also eligible to participate in our amended and restated 2003 stock incentive plan. In August 2003, the board of directors adopted a program under which each
non-employee director is eligible to receive an option to purchase 20,000 shares of our common stock upon his appointment to the board and also is eligible to receive an annual grant of an
option to purchase 10,000 shares of our common stock at each year's annual meeting at which he serves as a director. All options granted under our director option program vest in four equal annual
installments beginning on the first anniversary of the grant date. Each option terminates on the earlier of ten years from the date of grant or 90 days after the optionee ceases to serve as a
director, except in the case of death or disability, in which event the option terminates three months from the date of the director's death or disability.

7

---



Mr. Loberg's
options terminate one year from his death or disability. The exercise price of these options equals the fair market value of our common stock on the date of grant.

In
accordance with our director stock option program in effect in 2003, in November 2003 we granted Mr. Scoon an option to purchase 20,000 shares of our common stock at an
exercise price of $8.90 per share, which was the closing sale price of our common stock, as reported on the NASDAQ National Market, on the date of grant, upon his appointment to the board of
directors.

For
information regarding consulting fees paid to members of our board of directors, see "Item 13. Certain Relationships and Related TransactionsConsulting Arrangements."

Compensation Committee Interlocks and Insider Participation

The members of the Compensation Committee during the fiscal year ended December 31, 2003 were Dr. Karabelas and Messrs. Cohen and Leschly. No
member of the Compensation Committee was at any time during the fiscal year ended December 31, 2003, or formerly, an officer or employee of NitroMed or any subsidiary of NitroMed, nor has any
member of the Compensation Committee had any relationship with NitroMed during the fiscal year ended December 31, 2003 requiring disclosure under Item 404 of Regulation S-K
under the Securities Exchange Act of 1934.

None
of our executive officers has served as a director or member of the compensation committee (or other committee serving an equivalent function) of any other entity, one of whose
executive officers served as a director of or member of the Compensation Committee of NitroMed.

8

---





ITEM 12. SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT AND RELATED STOCKHOLDER MATTERS

Security Ownership

The following table sets forth information regarding beneficial ownership of our common stock as of April 16, 2004 by:



The
number of shares of common stock beneficially owned by each person or entity is determined in accordance with the applicable rules of the Securities and Exchange Commission and
includes voting or investment power with respect to shares of our common stock. The information is not necessarily indicative of beneficial ownership for any other purpose. Unless otherwise indicated,
to our knowledge, all persons named in the table have sole voting and investment power with respect to their shares of common stock, except to the extent authority is shared by spouses under community
property laws. The

9

---



inclusion
of any shares deemed beneficially owned in this table does not constitute an admission of beneficial ownership of those shares.

|Name and Address of Beneficial Owner (1)                                                            |  | Number of
Shares Owned |  | Common Stock
Underlying Options
Acquirable Within
60 Days |  | Total
Beneficial
Ownership |  | Percentage of
Common Stock
Beneficially
Owned (2)
|--------------------------------------------------------------------------------------------------- |  | ---------------------- |  | --------------------------------------------------------- |  | -------------------------- |  | -------------------------------------------------
|5% Stockholders                                                                                     |  |                        |  |                                                           |  |                            |  |                                                  
|Funds Managed by HealthCare Ventures, L.L.C. (3)
44 Nassau Street, Second Floor
Princeton, NJ 08837 |  | 6,354,103              |  |                                                          |  | 6,354,103                  |  | 24.8                                             
|Rho Ventures (4)
152 West 57th Street, 23rd Floor
New York, NY 10019                                |  | 5,469,333              |  |                                                          |  | 5,469,333                  |  | 21.3                                             
|Funds Managed by Care Capital LLC (5)
47 Hullfish Street, Suite 310
Princeton, NJ 08542             |  | 2,051,533              |  |                                                          |  | 2,051,533                  |  | 8.0                                              
|Delaware Management Holdings (6)
2005 Market Street
Philadelphia, PA 19103                          |  | 2,044,300              |  |                                                          |  | 2,044,300                  |  | 8.0                                              
|Johnson & Johnson Development Corporation
One Johnson & Johnson Plaza
New Brunswick, NJ 08933       |  | 1,342,207              |  |                                                          |  | 1,342,207                  |  | 5.2                                              
|Directors and Named Executive Officers                                                              |  |                        |  |                                                           |  |                            |  |                                                  
|Michael D. Loberg, Ph.D. (7)                                                                        |  | 359,384                |  | 233,970                                                   |  | 593,354                    |  | 2.3                                              
|Manuel Worcel                                                                                       |  | 53,758                 |  | 328,310                                                   |  | 382,068                    |  | 1.5                                              
|L. Gordon Letts, Ph.D.                                                                              |  | 100,125                |  | 200,160                                                   |  | 300,285                    |  | 1.2                                              
|Joseph Grimm                                                                                        |  | 34,383                 |  | 123,632                                                   |  | 158,015                    |  | *                                                
|Robert S. Cohen                                                                                     |  |                       |  | 25,000                                                    |  | 25,000                     |  | *                                                
|Argeris Karabelas, Ph.D. (8)                                                                        |  | 2,051,533              |  | 7,500                                                     |  | 2,059,033                  |  | 8.0                                              
|Zola Horovitz, Ph.D.                                                                                |  |                       |  | 25,000                                                    |  | 25,000                     |  | *                                                
|Mark Leschly (9)                                                                                    |  | 5,489,333              |  |                                                          |  | 5,489,333                  |  | 21.4                                             
|John W. Littlechild (10)                                                                            |  | 6,361,603              |  | 5,625                                                     |  | 6,367,228                  |  | 24.8                                             
|Joseph Loscalzo                                                                                     |  | 3,449                  |  | 72,551                                                    |  | 76,000                     |  | *                                                
|Davey S. Scoon                                                                                      |  |                       |  |                                                          |  |                           |  | *                                                
|All directors and executive officers as a group (11 persons)                                        |  | 14,453,568             |  | 1,021,748                                                 |  | 15,475,316                 |  | 60.3                                             

---

10

---





11

---



Securities Authorized for Issuance Under Equity Compensation Plans

The following table provides information as of December 31, 2003 about the securities authorized for issuance under our equity compensation plans,
consisting of our 1993 Equity Incentive Plan, our Amended and Restated 2003 Stock Incentive Plan, and our 2003 Employee Stock Purchase Plan. All of our equity compensation plans were adopted with the
approval of our stockholders.

Equity Compensation Plan Information

|Plan Category                                          |  | Number of Securities to be
Issued Upon Exercise of
Outstanding Options,
Warrants and Rights |  | Weighted-average Exercise
Price of Outstanding Options,
Warrants and Rights |      | Number of Securities Remaining
Available for Future Issuance
Under Equity Compensation
Plans (Excluding Securities
Reflected in Column (a)) (1)
|------------------------------------------------------ |  | ------------------------------------------------------------------------------------------- |  | --------------------------------------------------------------------------- | ---- | -----------------------------------------------------------------------------------------------------------------------------------------------
|
|Equity compensation plans approved by stockholders     |  | 2,898,584                                                                                   |  | $                                                                           | 2.62 |                                                                                                                                                
|Equity compensation plans not approved by stockholders |  |                                                                                            |  |                                                                             |     |                                                                                                                                                
|                                                       |  |                                                                                             |  |                                                                             |      |                                                                                                                                                
|Total:                                                 |  | 2,898,584                                                                                   |  | $                                                                           | 2.62 |                                                                                                                                                

---

12

---





ITEM 13. CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS

Issuance of Series E Convertible Preferred Stock

In August 2003, we sold an aggregate of 2,776,347 shares of our series E convertible preferred stock at a price per share of $7.2037 for an
aggregate purchase price of approximately $19.9 million. Of these 2,776,347 shares, an aggregate of 2,639,365 shares of series E convertible preferred stock were sold to the directors,
officers and five percent stockholders and their affiliates named below. These shares automatically converted into shares of our common stock upon the closing of our initial public offering on
November 11, 2003 at a conversion ratio of 1.1526 shares of common stock for each share of series E convertible preferred stock then held.

|Name                                             |        | Series E Convertible
Preferred Stock |           | Purchase Price
|------------------------------------------------ | ------ | ------------------------------------ | --------- | --------------
|Rho Ventures (1)                                 |        | 1,665,808                            |           | $             
|Funds managed by HealthCare Ventures, L.L.C. (2) |        | 416,452                              |           |               
|Funds managed by Care Capital LLC (3)            |        | 557,105                              |           |               
|                                                 |        |                                      |           |               
|                                                 | Total: |                                      | 2,639,365 |               

---

Registration Rights

Certain holders of our common stock, including shares of our common stock underlying warrants, are entitled to require us to register their shares of common stock
or participate in a registration of shares of common stock by us under the Securities Act of 1933. These rights are provided under the

13

---



terms
of stockholders' agreements between us and these holders. These holders include the following directors, officers and holders of more than five percent of our voting securities and their
affiliates:

Name of Holder

Number of Registrable
Shares of Common StockFunds managed by HealthCare Ventures, L.L.C. (1)

6,354,103Rho Ventures (2)

5,169,375Funds managed by Care Capital LLC (3)

2,051,533Johnson & Johnson Development Corporation

1,342,207Michael D. Loberg

286,608Joseph Grimm

34,383Manuel Worcel

23,289Total:

15,261,498


---

Boston University

Dr. Loscalzo, a member of our board of directors, is the Chairman of the Department of Medicine at Boston University Medical School,
Physician-in-Chief, Boston Medical Center and Director of the Whitaker Cardiovascular Institute at the Boston Medical Center.

Dr. Loscalzo
has served as a consultant since 1992 and as the chair of our scientific advisory board since 1999. In October 2003, we entered into a consulting agreement
with Dr. Loscalzo, as amended in April 2004, pursuant to which we have agreed to pay Dr. Loscalzo an annual retainer of $55,000 for his services. The agreement is for a period of
ten years, subject to the Company's right to terminate the agreement at any time on 30 days' notice. In 2003, we paid Dr. Loscalzo an aggregate of $70,000.

In
June 1993, as amended in January 1999 and May 2003, we entered into a research and license agreement with the Trustees of Boston University, or BU. Under the
agreement, we have agreed to fund a multi-year research program under Dr. Loscalzo's direction at BU in the area of nitric oxide-enhancing medicines. Our funding is principally for
laboratory equipment and supplies as well as a portion of the salary of Martin Feelish, Ph.D., a professor of medicine at BU and a member of our scientific advisory board. We have also agreed to
provide Dr. Feelish with access to our research facilities at the BU School of Medicine. Under the agreement, in exchange for our sponsored research funding, BU has granted us exclusive
worldwide royalty-bearing rights to technology and inventions owned by BU at the effective time of, or developed in the course of, the sponsored research program. We have agreed to pay royalties to BU
on all products sold or distributed by us or our affiliates which incorporate or utilize inventions, material or information specified in the agreement. In 2003, we made payments to BU in the amount
of $295,750 pursuant to this agreement, excluding the lease payments described below.

14

---



In
May 2003, we entered into an oral agreement with BU pursuant to which we lease approximately 1,500 square feet of laboratory space from BU at its Evans Biomedical Research
Center in Boston, Massachusetts. The lease has a term of three years and we make annual rental payments of $60,000 pursuant to the lease. As provided above, we have agreed to make this space available
to Dr. Feelish of BU. In 2003, we made payments to BU under this agreement in the amount of $30,000.

For
executive officer compensation and option exercise information, see "Item 11. Executive Compensation."

ITEM 14. PRINCIPAL ACCOUNTANT FEES AND SERVICES

Independent Auditor's Fees

The following table summarizes the fees of Ernst & Young LLP, our independent auditor, billed to us for each of the last two fiscal years for audit
services and billed to us in each of the last two years for other services:

Fee Category

2003

2002Audit Fees (1)

$
442,700

$
48,000Audit-Related Fees





Tax Fees (2)


11,300


11,300All Other Fees





Total Fees

$
454,000

$
59,300


---

Pre-Approval Policy and Procedures

The Audit Committee has adopted policies and procedures relating to the approval of all audit and non-audit services that are to be performed by our
independent auditor. This policy generally provides that we will not engage our independent auditor to render audit or non-audit services unless the service is specifically approved in
advance by the Audit Committee or the engagement is entered into pursuant to one of the pre-approval procedures described below.

From
time to time, the Audit Committee may pre-approve specified types of services that are expected to be provided to us by our independent auditor during the next
12 months. Any such pre-approval is detailed as to the particular service or type of services to be provided and is also generally subject to a maximum dollar amount.

The
Audit Committee has also delegated to the chairman of the Audit Committee the authority to approve any audit or non-audit services to be provided to us by our independent
auditor. Any approval of services by a member of the Audit Committee pursuant to this delegated authority is reported on at the next meeting of the Audit Committee.

15

---





PART IV

ITEM 15. EXHIBITS, FINANCIAL STATEMENT SCHEDULES, AND REPORTS ON FORM 8-K

|Exhibit No. |  | Description                                                                                                                                                                                        
|----------- |  | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|31.1        |  | Certification of the Chief Executive Officer pursuant to Rule 13a-14(a) and 15d-14(a) 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(a) of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.

16

---





SIGNATURES

Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its
behalf by the undersigned.

|                     |  | NITROMED, INC.
|-------------------- |  | --------------
|Date: April 29, 2004 |  | By:           

17

---



QuickLinks