| Round | Overall | Player |
|---|---|---|
| 1 | 9th | DH Jim Thome ChA |
| 2 | 16th | SP Jason Schmidt SF |
| 3 | 33rd | SP Mark Prior ChN |
| 4 | 40th | 2B Marcus Giles Atl |
| 5 | 57th | RP Joe Nathan Min |
| 6 | 64th | OF Garret Anderson LAA |
| 7 | 81st | 3B Mike Lowell Fla |
| 8 | 88th | OF Steve Finley LAA |
| 9 | 105th | SS Orlando Cabrera LAA |
| 10 | 112th | SP Javier Vazquez Ari |
| 11 | 129th | OF Corey Patterson ChN |
| 12 | 136th | SP Brad Radke Min |
| 13 | 153rd | SP Andy Pettitte Hou |
| 14 | 160th | OF Torii Hunter Min |
| 15 | 177th | C Johnny Estrada Atl |
| 16 | 184th | 1B Dmitri Young Det |
| 17 | 201st | SP Cliff Lee Cle |
| 18 | 208th | SP Kevin Millwood Cle |
| 19 | 225th | OF Craig A. Wilson Pit |
| 20 | 232nd | SS Melvin Upton TB |
| 21 | 249th | C Michael Barrett ChN |
| 22 | 256th | SP Dan Haren Oak |
| 23 | 273rd | 2B Keith Ginter Oak |
| 24 | 280th | DH Shea Hillenbrand Tor |
| 25 | 297th | 3B Brandon Inge Det |
| 26 | 304th | SP Jeff Francis Col |
| 27 | 321st | OF Jerry Hairston Jr. ChN |
| 28 | 328th | SP Jason Frasor Tor |
| 29 | 345th | 1B Casey Kotchman LAA |