| Round | Overall | Player |
|---|---|---|
| 1 | 2nd | 3B Alex Rodriguez NYA |
| 2 | 23rd | 1B Adam Dunn Cin |
| 3 | 26th | RP Eric Gagne LAD |
| 4 | 47th | 2B Marcus Giles Atl |
| 5 | 50th | OF Aubrey Huff TB |
| 6 | 71st | C Mike Piazza NYN |
| 7 | 74th | OF Jason Bay Pit |
| 8 | 95th | RP Troy Percival Det |
| 9 | 98th | SP Josh Beckett Fla |
| 10 | 119th | 1B Sean Casey Cin |
| 11 | 122nd | SS Rafael Furcal Atl |
| 12 | 143rd | OF Kevin Mench Tex |
| 13 | 146th | RP Jose Mesa Pit |
| 14 | 167th | SP Horacio Ramirez Atl |
| 15 | 170th | SP Derek Lowe LAD |
| 16 | 191st | SP Brian Lawrence SD |
| 17 | 194th | 1B Lyle Overbay Mil |
| 18 | 215th | SP Paul Byrd LAA |
| 19 | 218th | SP Noah Lowry SF |
| 20 | 239th | SP Scott Kazmir TB |
| 21 | 242nd | SP Dan Haren Oak |
| 22 | 263rd | 3B Morgan Ensberg Hou |
| 23 | 266th | 1B Ryan Klesko SD |
| 24 | 287th | SP Jamie Moyer Sea |
| 25 | 290th | OF Milton Bradley LAD |
| 26 | 311th | SS Jhonny Peralta Cle |
| 27 | 314th | 1B Hee Seop Choi LAD |
| 28 | 335th | 2B Mark Grudzielanek StL |
| 29 | 338th | C Yadier Molina StL |