| Round | Overall | Player |
|---|---|---|
| 1 | 2nd | 1B Albert Pujols StL |
| 2 | 23rd | SP Roy Halladay Tor |
| 3 | 26th | 3B Morgan Ensberg Hou |
| 4 | 47th | OF Carl Crawford TB |
| 5 | 50th | SP Rich Harden Oak |
| 6 | 71st | OF Johnny Damon NYA |
| 7 | 74th | SP Ben Sheets Mil |
| 8 | 95th | RP Jason Isringhausen StL |
| 9 | 98th | C Jason Varitek Bos |
| 10 | 119th | SP Matt Morris SF |
| 11 | 122nd | SS Jose Reyes NYN |
| 12 | 143rd | SP Oliver Perez Pit |
| 13 | 146th | RP Trevor Hoffman SD |
| 14 | 167th | OF Nick Swisher Oak |
| 15 | 170th | DH Jose Vidro Was |
| 16 | 191st | 1B Lyle Overbay Tor |
| 17 | 194th | OF Milton Bradley Oak |
| 18 | 215th | SP Odalis Perez KC |
| 19 | 218th | 1B Shea Hillenbrand LAA |
| 20 | 239th | SP Gustavo Chacin Tor |
| 21 | 242nd | 2B Ray Durham SF |
| 22 | 263rd | OF Jeromy Burnitz Pit |
| 23 | 266th | SP Adam Eaton Phi |
| 24 | 287th | SS Omar Vizquel SF |
| 25 | 290th | 3B Aaron Boone Cle |
| 26 | 311th | SP Jamie Moyer Phi |
| 27 | 314th | RP Mike MacDougal ChA |
| 28 | 335th | OF David DeJesus KC |
| 29 | 338th | OF Xavier Nady Pit |