| Round | Overall | Player |
|---|---|---|
| 1 | 11th | DH Jim Thome ChA |
| 2 | 14th | OF Manny Ramirez Bos |
| 3 | 35th | SS Derek Jeter NYA |
| 4 | 38th | RP Keith Foulke Bos |
| 5 | 59th | OF Brian S. Giles SD |
| 6 | 62nd | RP Joe Nathan Min |
| 7 | 83rd | OF Carlos Lee Mil |
| 8 | 86th | SP Roy Halladay Tor |
| 9 | 107th | 3B David Wright NYN |
| 10 | 110th | SP Javier Vazquez Ari |
| 11 | 131st | DH Mike Sweeney KC |
| 12 | 134th | 2B Jose Vidro Was |
| 13 | 155th | SP Matt Morris StL |
| 14 | 158th | SP Greg Maddux ChN |
| 15 | 179th | C Johnny Estrada Atl |
| 16 | 182nd | OF Jose Guillen Was |
| 17 | 203rd | SS Orlando Cabrera LAA |
| 18 | 206th | 3B Pedro Feliz SF |
| 19 | 227th | SP Jarrod Washburn LAA |
| 20 | 230th | OF Trot Nixon Bos |
| 21 | 251st | 2B Aaron Miles Col |
| 22 | 254th | C A.J. Pierzynski ChA |
| 23 | 275th | 1B Eric Hinske Tor |
| 24 | 278th | SP Ted Lilly Tor |
| 25 | 299th | OF Jason Lane Hou |
| 26 | 302nd | SP Kip Wells Pit |
| 27 | 323rd | SP Brett Tomko SF |
| 28 | 326th | SP Luke Hudson Cin |
| 29 | 347th | SP Mike Gonzalez Pit |