| Round | Overall | Player |
|---|---|---|
| 1 | 6th | OF Vladimir Guerrero LAA |
| 2 | 19th | OF Gary Sheffield Det |
| 3 | 30th | SS Derek Jeter NYA |
| 4 | 43rd | SP Bartolo Colon LAA |
| 5 | 54th | C Joe Mauer Min |
| 6 | 67th | 2B Marcus Giles Atl |
| 7 | 78th | OF Barry Bonds SF |
| 8 | 91st | 3B Scott Rolen StL |
| 9 | 102nd | SP Brandon Webb Ari |
| 10 | 115th | SP Brett Myers Phi |
| 11 | 126th | C Ivan Rodriguez Det |
| 12 | 139th | OF J.D. Drew LAD |
| 13 | 150th | 1B Prince Fielder Mil |
| 14 | 163rd | RP Eddie Guardado Cin |
| 15 | 174th | SP Noah Lowry SF |
| 16 | 187th | RP Mike Gonzalez Atl |
| 17 | 198th | 2B Mark Loretta Bos |
| 18 | 211th | RP Chris Ray Bal |
| 19 | 222nd | OF Randy Winn SF |
| 20 | 235th | SP Kris Benson Bal |
| 21 | 246th | SS David Eckstein StL |
| 22 | 259th | 1B Shea Hillenbrand LAA |
| 23 | 270th | 3B Brandon Inge Det |
| 24 | 283rd | SP Kenny Rogers Det |
| 25 | 294th | OF Chris Duffy Pit |
| 26 | 307th | SP David Wells SD |
| 27 | 318th | C Yorvit Torrealba Col |
| 28 | 331st | RP Joe Borowski Cle |
| 29 | 342nd | SP Adam Eaton Phi |