| Round | Overall | Player |
|---|---|---|
| 1 | 12th | OF Lance Berkman Hou |
| 2 | 13th | 1B Jim Thome Phi |
| 3 | 36th | OF Larry Walker Col |
| 4 | 37th | OF Carlos Beltran KC |
| 5 | 60th | RP Keith Foulke Oak |
| 6 | 61st | SP Mark Prior ChN |
| 7 | 84th | OF Hideki Matsui NYA |
| 8 | 85th | RP Eddie Guardado Min |
| 9 | 108th | 2B Junior Spivey Ari |
| 10 | 109th | 3B Joe Crede ChA |
| 11 | 132nd | SS Jose Valentin ChA |
| 12 | 133rd | DH Josh Phelps Tor |
| 13 | 156th | SP Kazuhisa Ishii LA |
| 14 | 157th | SP John Lackey Ana |
| 15 | 180th | SP Jason Simontacchi StL |
| 16 | 181st | RP Byung-Hyun Kim Bos |
| 17 | 204th | SP Tomo Ohka Mon |
| 18 | 205th | SP Kip Wells Pit |
| 19 | 228th | C Michael Barrett Mon |
| 20 | 229th | SP Johan Santana Min |
| 21 | 252nd | SP Mark Redman Fla |
| 22 | 253rd | SP Kyle Lohse Min |
| 23 | 276th | 1B Hee Seop Choi ChN |
| 24 | 277th | 3B Jeff Cirillo Sea |
| 25 | 300th | OF Kenny Lofton ChN |
| 26 | 301st | C Josh Bard Cle |
| 27 | 324th | SS Juan Uribe Col |
| 28 | 325th | 2B D'Angelo Jimenez Cin |
| 29 | 348th | OF Dmitri Young Det |