| Round | Overall | Player |
|---|---|---|
| 1 | 10th | SS Mike Young Tex |
| 2 | 15th | 2B Chase Utley Phi |
| 3 | 34th | SP Roy Oswalt Hou |
| 4 | 39th | OF Hideki Matsui NYA |
| 5 | 58th | RP Francisco Rodriguez LAA |
| 6 | 63rd | 3B Morgan Ensberg Hou |
| 7 | 82nd | C Jason Varitek Bos |
| 8 | 87th | 1B Jason Giambi NYA |
| 9 | 106th | 1B Justin Morneau Min |
| 10 | 111th | SP Curt Schilling Bos |
| 11 | 130th | SP Freddy Garcia ChA |
| 12 | 135th | OF Magglio Ordonez Det |
| 13 | 154th | SP Matt Cain SF |
| 14 | 159th | RP Ryan Dempster ChN |
| 15 | 178th | RP Armando Benitez SF |
| 16 | 183rd | OF Jermaine Dye ChA |
| 17 | 202nd | SP Oliver Perez Pit |
| 18 | 207th | OF Garret Anderson LAA |
| 19 | 226th | SP Odalis Perez KC |
| 20 | 231st | C Ben Molina SF |
| 21 | 250th | DH Frank Thomas Oak |
| 22 | 255th | 1B Shea Hillenbrand LAA |
| 23 | 274th | OF David Dellucci Cle |
| 24 | 279th | SP Steve Trachsel NYN |
| 25 | 298th | SS Juan Uribe ChA |
| 26 | 303rd | RP Joel Pineiro Bos |
| 27 | 322nd | SP Brandon McCarthy Tex |
| 28 | 327th | 2B Jose Castillo Pit |
| 29 | 346th | 3B Joe Randa Pit |