| Round | Overall | Player |
|---|---|---|
| 1 | 10th | SP Pedro Martinez Bos |
| 2 | 15th | OF Albert Pujols StL |
| 3 | 34th | SS Edgar Renteria StL |
| 4 | 39th | 1B Mike Sweeney KC |
| 5 | 58th | 2B Ray Durham SF |
| 6 | 63rd | RP Eddie Guardado Min |
| 7 | 82nd | 3B Corey Koskie Min |
| 8 | 87th | SP Javier Vazquez Mon |
| 9 | 106th | RP Ugueth Urbina Fla |
| 10 | 111th | OF Juan Gonzalez Tex |
| 11 | 130th | 3B Jose Hernandez Pit |
| 12 | 135th | C Javy Lopez Atl |
| 13 | 154th | SP Woody Williams StL |
| 14 | 159th | 1B Aubrey Huff TB |
| 15 | 178th | RP Byung-Hyun Kim Bos |
| 16 | 183rd | OF Darin Erstad Ana |
| 17 | 202nd | C Michael Barrett Mon |
| 18 | 207th | SP Joe Mays Min |
| 19 | 226th | SP Oliver Perez SD |
| 20 | 231st | 2B Adam Kennedy Ana |
| 21 | 250th | SP Jake Peavy SD |
| 22 | 255th | SP Jose Contreras NYA |
| 23 | 274th | OF Juan Pierre Fla |
| 24 | 279th | SS Pablo Ozuna Col |
| 25 | 298th | OF Danny Bautista Ari |
| 26 | 303rd | RP Braden Looper Fla |
| 27 | 322nd | SP Victor Zambrano TB |
| 28 | 327th | OF Melvin Mora Bal |
| 29 | 346th | 1B David Ortiz Bos |