| Round | Overall | Player |
|---|---|---|
| 1 | 9th | SS Jose Reyes NYN |
| 2 | 16th | OF Carl Crawford TB |
| 3 | 33rd | SP Chris Carpenter StL |
| 4 | 40th | OF Jermaine Dye ChA |
| 5 | 57th | SP Brett Myers Phi |
| 6 | 64th | SP C.C. Sabathia Cle |
| 7 | 81st | 1B Adrian Gonzalez SD |
| 8 | 88th | SP Erik Bedard Bal |
| 9 | 105th | OF Alexis Rios Tor |
| 10 | 112th | RP Tom Gordon Phi |
| 11 | 129th | RP Jason Isringhausen StL |
| 12 | 136th | 1B Adam LaRoche Pit |
| 13 | 153rd | 3B Chad Tracy Ari |
| 14 | 160th | SP Ervin Santana LAA |
| 15 | 177th | OF Brad Hawpe Col |
| 16 | 184th | C Ivan Rodriguez Det |
| 17 | 201st | 2B Orlando Hudson Ari |
| 18 | 208th | SP Carl Pavano NYA |
| 19 | 225th | RP Akinori Otsuka Tex |
| 20 | 232nd | OF Carlos Quentin ChA |
| 21 | 249th | 3B Mike Lowell Bos |
| 22 | 256th | SP Anthony Reyes StL |
| 23 | 273rd | 2B Mark DeRosa ChN |
| 24 | 280th | SS Yuniesky Betancourt Sea |
| 25 | 297th | RP Clay Hensley SD |
| 26 | 304th | OF Coco Crisp Bos |
| 27 | 321st | C Miguel Olivo Fla |
| 28 | 328th | 1B Doug Mientkiewicz NYA |
| 29 | 345th | SP Gustavo Chacin Tor |