| Round | Overall | Player |
|---|---|---|
| 1 | 5th | OF Vladimir Guerrero Mon |
| 2 | 20th | 1B Jim Thome Phi |
| 3 | 29th | 3B Scott Rolen StL |
| 4 | 44th | SP Mark Buehrle ChA |
| 5 | 53rd | 2B Jose Vidro Mon |
| 6 | 68th | SP Kevin Millwood Phi |
| 7 | 77th | OF Vernon Wells Tor |
| 8 | 92nd | RP Jason Isringhausen StL |
| 9 | 101st | OF Cliff Floyd NYN |
| 10 | 116th | SS Cristian Guzman Min |
| 11 | 125th | SP Russ Ortiz Atl |
| 12 | 140th | OF Moises Alou ChN |
| 13 | 149th | 3B Brandon Larson Cin |
| 14 | 164th | SP Jon Garland ChA |
| 15 | 173rd | OF J.D. Drew StL |
| 16 | 188th | C Jason Varitek Bos |
| 17 | 197th | 1B Hee Seop Choi ChN |
| 18 | 212th | SP Damian Moss Bal |
| 19 | 221st | 2B Luis Rivas Min |
| 20 | 236th | SP Jason Simontacchi StL |
| 21 | 245th | SP Brandon Duckworth Phi |
| 22 | 260th | OF Eli Marrero StL |
| 23 | 269th | DH Nick Johnson NYA |
| 24 | 284th | OF Corey Patterson ChN |
| 25 | 293rd | C Ben Davis Sea |
| 26 | 308th | 3B Bill Mueller Bos |
| 27 | 317th | SP Omar Daal Bal |
| 28 | 332nd | OF Daryle Ward LA |
| 29 | 341st | SS Ramon Vazquez SD |