| Round | Overall | Player |
|---|---|---|
| 1 | 5th | 1B Ryan Howard Phi |
| 2 | 20th | 3B Garrett Atkins Col |
| 3 | 29th | OF Carl Crawford TB |
| 4 | 44th | OF Jermaine Dye ChA |
| 5 | 53rd | DH Jim Thome ChA |
| 6 | 68th | SP Jon Papelbon Bos |
| 7 | 77th | SP Daisuke Matsuzaka Bos |
| 8 | 92nd | RP Bobby Jenks ChA |
| 9 | 101st | SP Randy Johnson Ari |
| 10 | 116th | 2B Rickie Weeks Mil |
| 11 | 125th | SP Roger Clemens NYA |
| 12 | 140th | SS Julio Lugo Bos |
| 13 | 149th | C Ivan Rodriguez Det |
| 14 | 164th | OF Jim Edmonds SD |
| 15 | 173rd | RP Brian Fuentes Col |
| 16 | 188th | SP Jose Contreras ChA |
| 17 | 197th | OF Chris Duncan StL |
| 18 | 212th | SP Javier Vazquez ChA |
| 19 | 221st | SP Pedro Martinez NYN |
| 20 | 236th | OF Juan Pierre LAD |
| 21 | 245th | 1B Shea Hillenbrand LAD |
| 22 | 260th | RP Josh Johnson Fla |
| 23 | 269th | SS Omar Vizquel SF |
| 24 | 284th | SP Mark Prior ChN |
| 25 | 293rd | 3B Andy Marte Cle |
| 26 | 308th | C Jason Kendall Mil |
| 27 | 317th | 2B Adam Kennedy StL |
| 28 | 332nd | SP Esteban Loaiza LAD |
| 29 | 341st | SP Shawn Hill Was |