| Round | Overall | Player |
|---|---|---|
| 1 | 12th | OF Vladimir Guerrero Ana |
| 2 | 13th | C Jorge Posada NYA |
| 3 | 36th | SP Tim Hudson Oak |
| 4 | 37th | RP Billy Wagner Phi |
| 5 | 60th | 1B Derrek Lee ChN |
| 6 | 61st | SP Kevin Millwood Phi |
| 7 | 84th | RP Troy Percival Ana |
| 8 | 85th | SS Angel Berroa KC |
| 9 | 108th | OF Luis Gonzalez Ari |
| 10 | 109th | SP Greg Maddux ChN |
| 11 | 132nd | OF J.D. Drew Atl |
| 12 | 133rd | 2B Placido Polanco Phi |
| 13 | 156th | 1B Shea Hillenbrand Ari |
| 14 | 157th | OF Bernie Williams NYA |
| 15 | 180th | SP Kyle Lohse Min |
| 16 | 181st | SP Gil Meche Sea |
| 17 | 204th | OF Carl Everett ChA |
| 18 | 205th | 2B Todd Walker ChN |
| 19 | 228th | OF Marlon Byrd Phi |
| 20 | 229th | SP Brian Lawrence SD |
| 21 | 252nd | 1B Jeff Conine Fla |
| 22 | 253rd | SP Edwin Jackson LA |
| 23 | 276th | SS Alex Gonzalez Fla |
| 24 | 277th | SP Aquilino Lopez Tor |
| 25 | 300th | SP Jason Johnson Det |
| 26 | 301st | 3B Ty Wigginton Pit |
| 27 | 324th | OF Jay Payton SD |
| 28 | 325th | C Jason LaRue Cin |
| 29 | 348th | SP Jason Marquis StL |