| Round | Overall | Player |
|---|---|---|
| 1 | 5th | 1B Ryan Howard Phi |
| 2 | 20th | SS Miguel Tejada Hou |
| 3 | 29th | 3B Aramis Ramirez ChN |
| 4 | 44th | DH Jim Thome ChA |
| 5 | 53rd | OF Johnny Damon NYA |
| 6 | 68th | OF J.D. Drew Bos |
| 7 | 77th | 2B Brian Roberts Bal |
| 8 | 92nd | 3B Scott Rolen StL |
| 9 | 101st | SP Josh Beckett Bos |
| 10 | 116th | OF Alexis Rios Tor |
| 11 | 125th | C Ramon Hernandez Bal |
| 12 | 140th | SP Ervin Santana LAA |
| 13 | 149th | OF Josh Willingham Fla |
| 14 | 164th | SP Chris Capuano Mil |
| 15 | 173rd | SP Mark Buehrle ChA |
| 16 | 188th | RP Akinori Otsuka Tex |
| 17 | 197th | RP Jorge Julio Col |
| 18 | 212th | SP Nate Robertson Det |
| 19 | 221st | SP Jose Contreras ChA |
| 20 | 236th | SP Pedro Martinez NYN |
| 21 | 245th | RP Salomon Torres Mil |
| 22 | 260th | OF Jacque Jones Det |
| 23 | 269th | C David Ross Cin |
| 24 | 284th | 1B Sean Casey Det |
| 25 | 293rd | 2B Jose Castillo Pit |
| 26 | 308th | SS Yuniesky Betancourt Sea |
| 27 | 317th | SP Aaron Cook Col |
| 28 | 332nd | SP Randy Wolf SD |
| 29 | 341st | SP Horacio Ramirez Sea |