| Round | Overall | Player |
|---|---|---|
| 1 | 2nd | OF Vladimir Guerrero Mon |
| 2 | 23rd | SP Roy Oswalt Hou |
| 3 | 26th | OF Bobby Abreu Phi |
| 4 | 47th | SP Mike Mussina NYA |
| 5 | 50th | RP Eric Gagne LA |
| 6 | 71st | RP Armando Benitez Sea |
| 7 | 74th | 1B Ryan Klesko SD |
| 8 | 95th | 3B Edgardo Alfonzo SF |
| 9 | 98th | 2B Aaron Boone NYA |
| 10 | 119th | SP Matt Clement ChN |
| 11 | 122nd | RP Jason Isringhausen StL |
| 12 | 143rd | DH Frank Thomas ChA |
| 13 | 146th | SP Josh Beckett Fla |
| 14 | 167th | SS Cristian Guzman Min |
| 15 | 170th | SP Kris Benson Pit |
| 16 | 191st | OF Jose Cruz Jr SF |
| 17 | 194th | SP Rick Reed Min |
| 18 | 215th | 1B Carlos Pena Det |
| 19 | 218th | OF Juan Encarnacion Fla |
| 20 | 239th | 2B Eric Young SF |
| 21 | 242nd | C Brad Ausmus Hou |
| 22 | 263rd | SP Jon Garland ChA |
| 23 | 266th | OF Jay Gibbons Bal |
| 24 | 287th | DH Nick Johnson NYA |
| 25 | 290th | OF Craig Biggio Hou |
| 26 | 311th | C Ben Davis Sea |
| 27 | 314th | SS Julio Lugo TB |
| 28 | 335th | 1B Jeff Liefer TB |
| 29 | 338th | 3B Ty Wigginton NYN |