| Round | Overall | Player |
|---|---|---|
| 1 | 4th | OF Barry Bonds SF |
| 2 | 21st | OF Magglio Ordonez ChA |
| 3 | 28th | 3B Troy Glaus Ana |
| 4 | 45th | 1B Jeff Bagwell Hou |
| 5 | 52nd | SP Mike Mussina NYA |
| 6 | 69th | RP Billy Wagner Hou |
| 7 | 76th | 2B Bret Boone Sea |
| 8 | 93rd | SS Rich Aurilia SF |
| 9 | 100th | RP Kelvim Escobar Tor |
| 10 | 117th | OF Vernon Wells Tor |
| 11 | 124th | SP Russ Ortiz Atl |
| 12 | 141st | C A.J. Pierzynski Min |
| 13 | 148th | RP Jason Isringhausen StL |
| 14 | 165th | 2B Orlando Hudson Tor |
| 15 | 172nd | SP Joe Mays Min |
| 16 | 189th | SP David Wells NYA |
| 17 | 196th | SP Damian Moss Bal |
| 18 | 213th | 3B Brandon Larson Cin |
| 19 | 220th | C Ramon Hernandez Oak |
| 20 | 237th | SS Alex Gonzalez ChN |
| 21 | 244th | SP Brandon Duckworth Phi |
| 22 | 261st | 1B Doug Mientkiewicz Min |
| 23 | 268th | 3B Xavier Nady SD |
| 24 | 285th | SP Jon Garland ChA |
| 25 | 292nd | OF Craig Biggio Hou |
| 26 | 309th | SP Eric Milton Min |
| 27 | 316th | C Joe Mauer Min |
| 28 | 333rd | SP Jesse Foppert SF |
| 29 | 340th | OF Carl Crawford TB |