| Round | Overall | Player |
|---|---|---|
| 1 | 12th | OF Luis Gonzalez Ari |
| 2 | 13th | OF Lance Berkman Hou |
| 3 | 36th | SP Mark Mulder Oak |
| 4 | 37th | OF Juan Gonzalez Tex |
| 5 | 60th | 1B Mo Vaughn NYN |
| 6 | 61st | SS Jimmy Rollins Phi |
| 7 | 84th | RP Troy Percival Ana |
| 8 | 85th | SS Cristian Guzman Min |
| 9 | 108th | 3B Jose Valentin ChA |
| 10 | 109th | 2B Jose Ortiz Col |
| 11 | 132nd | SP C.C. Sabathia Cle |
| 12 | 133rd | SP Andy Pettitte NYA |
| 13 | 156th | RP John Rocker Tex |
| 14 | 157th | OF Matt Lawton Cle |
| 15 | 180th | OF Robert Fick Det |
| 16 | 181st | SP Derek Lowe Bos |
| 17 | 204th | C Damian Miller Ari |
| 18 | 205th | 1B Derrek Lee Fla |
| 19 | 228th | SP Jason Marquis Atl |
| 20 | 229th | DH David Ortiz Min |
| 21 | 252nd | 2B Marlon Anderson Phi |
| 22 | 253rd | 3B Michael Cuddyer Min |
| 23 | 276th | SP Jon Garland ChA |
| 24 | 277th | SP Jeff Fassero ChN |
| 25 | 300th | SP Eric Gagne LA |
| 26 | 301st | OF Juan Encarnacion Cin |
| 27 | 324th | SP Ron Villone Pit |
| 28 | 325th | SP Kip Wells Pit |
| 29 | 348th | C Darrin Fletcher Tor |