| Round | Overall | Player |
|---|---|---|
| 1 | 9th | OF Jason Bay Pit |
| 2 | 16th | SP Johan Santana Min |
| 3 | 33rd | 2B Jeff Kent LAD |
| 4 | 40th | 1B Carlos Delgado NYN |
| 5 | 57th | 3B Hank Blalock Tex |
| 6 | 64th | SS Bobby Crosby Oak |
| 7 | 81st | SP Tim Hudson Atl |
| 8 | 88th | OF Jeff Francoeur Atl |
| 9 | 105th | SP C.C. Sabathia Cle |
| 10 | 112th | RP Francisco Cordero Mil |
| 11 | 129th | DH Javy Lopez Bos |
| 12 | 136th | OF Geoff Jenkins Mil |
| 13 | 153rd | RP Bob Wickman Atl |
| 14 | 160th | C Michael Barrett ChN |
| 15 | 177th | SP Jarrod Washburn Sea |
| 16 | 184th | 2B Ron Belliard StL |
| 17 | 201st | 3B Garrett Atkins Col |
| 18 | 208th | OF Raul Ibanez Sea |
| 19 | 225th | DH Dmitri Young Det |
| 20 | 232nd | SP Tom Glavine NYN |
| 21 | 249th | SS Orlando Cabrera LAA |
| 22 | 256th | OF Corey Patterson Bal |
| 23 | 273rd | SP Brad Radke Min |
| 24 | 280th | OF Emil Brown KC |
| 25 | 297th | C John Buck KC |
| 26 | 304th | SP Paul Maholm Pit |
| 27 | 321st | OF Juan Encarnacion StL |
| 28 | 328th | RP Joel Pineiro Bos |
| 29 | 345th | 1B Lance Niekro SF |