| Round | Overall | Player |
|---|---|---|
| 1 | 8th | SS Miguel Tejada Bal |
| 2 | 17th | SP Roy Halladay Tor |
| 3 | 32nd | 2B Marcus Giles Atl |
| 4 | 41st | SP Mark Prior ChN |
| 5 | 56th | 3B Hank Blalock Tex |
| 6 | 65th | C Javy Lopez Bal |
| 7 | 80th | SP Johan Santana Min |
| 8 | 89th | OF J.D. Drew Atl |
| 9 | 104th | RP Arthur Rhodes Oak |
| 10 | 113th | 1B Phil Nevin SD |
| 11 | 128th | SP Sidney Ponson Bal |
| 12 | 137th | OF Johnny Damon Bos |
| 13 | 152nd | RP Joe Nathan Min |
| 14 | 161st | OF Carl Everett ChA |
| 15 | 176th | 1B Nick Johnson Mon |
| 16 | 185th | SP Ted Lilly Tor |
| 17 | 200th | RP Mike MacDougal KC |
| 18 | 209th | SP Rich Harden Oak |
| 19 | 224th | OF Raul Mondesi Ana |
| 20 | 233rd | SP Rafael Soriano Sea |
| 21 | 248th | OF Randy Winn Sea |
| 22 | 257th | C Benito Santiago KC |
| 23 | 272nd | SS Khalil Greene SD |
| 24 | 281st | SP Kazuhisa Ishii LA |
| 25 | 296th | 3B Casey Blake Cle |
| 26 | 305th | SP Brandon Claussen Cin |
| 27 | 320th | SS Enrique Wilson NYA |
| 28 | 329th | OF Aaron Guiel KC |
| 29 | 344th | 2B Aaron Miles Col |