| Round | Overall | Player |
|---|---|---|
| 1 | 5th | OF Vladimir Guerrero Ana |
| 2 | 20th | SP Kerry Wood ChN |
| 3 | 29th | OF Vernon Wells Tor |
| 4 | 44th | OF Bobby Abreu Phi |
| 5 | 53rd | C Javy Lopez Bal |
| 6 | 68th | SP Andy Pettitte Hou |
| 7 | 77th | SS Orlando Cabrera Bos |
| 8 | 92nd | OF Miguel Cabrera Fla |
| 9 | 101st | 2B Ray Durham SF |
| 10 | 116th | 1B Kevin Millar Bos |
| 11 | 125th | RP Francisco Cordero Tex |
| 12 | 140th | RP Matt Mantei Ari |
| 13 | 149th | SP Jake Peavy SD |
| 14 | 164th | OF Rocco Baldelli TB |
| 15 | 173rd | SP Brett Myers Phi |
| 16 | 188th | 3B Sean Burroughs SD |
| 17 | 197th | SP Kip Wells Pit |
| 18 | 212th | RP Braden Looper NYN |
| 19 | 221st | SP Ted Lilly Tor |
| 20 | 236th | RP Robb Nen SF |
| 21 | 245th | SP Ryan Wagner Cin |
| 22 | 260th | 3B Eric Munson Det |
| 23 | 269th | 1B John Olerud NYA |
| 24 | 284th | SS Cristian Guzman Min |
| 25 | 293rd | C Miguel Olivo Sea |
| 26 | 308th | OF Craig A. Wilson Pit |
| 27 | 317th | SP Chad Cordero Mon |
| 28 | 332nd | 2B Orlando Hudson Tor |
| 29 | 341st | SP Oliver Perez Pit |