| Round | Overall | Player |
|---|---|---|
| 1 | 3rd | 1B Albert Pujols StL |
| 2 | 22nd | SS Derek Jeter NYA |
| 3 | 27th | C Mike Piazza NYN |
| 4 | 46th | SP Barry Zito Oak |
| 5 | 51st | OF Preston Wilson Col |
| 6 | 70th | OF Miguel Cabrera Fla |
| 7 | 75th | RP Eddie Guardado Sea |
| 8 | 94th | SS Jose Reyes NYN |
| 9 | 99th | SP Carlos Zambrano ChN |
| 10 | 118th | SP Jose Contreras ChA |
| 11 | 123rd | RP Ugueth Urbina Det |
| 12 | 142nd | OF Juan Pierre Fla |
| 13 | 147th | SS Alex Cintron Ari |
| 14 | 166th | 3B Bill Mueller Bos |
| 15 | 171st | 3B D'Angelo Jimenez Cin |
| 16 | 190th | SP Kip Wells Pit |
| 17 | 195th | OF Scott Podsednik Mil |
| 18 | 214th | SP Cory Lidle Phi |
| 19 | 219th | 1B Adam LaRoche Atl |
| 20 | 238th | RP Danny Graves Cin |
| 21 | 243rd | SP Cliff Lee Cle |
| 22 | 262nd | OF Juan Encarnacion Fla |
| 23 | 267th | SP Kris Benson NYN |
| 24 | 286th | SP A.J. Burnett Fla |
| 25 | 291st | C Ramon Castro Fla |
| 26 | 310th | 1B Justin Morneau Min |
| 27 | 315th | 1B Scott Spiezio Sea |
| 28 | 334th | SP John Lackey Ana |
| 29 | 339th | SS Melvin Upton TB |