| Round | Overall | Player |
|---|---|---|
| 1 | 12th | DH Travis Hafner Cle |
| 2 | 13th | 2B Chase Utley Phi |
| 3 | 36th | OF Carlos Beltran NYN |
| 4 | 37th | OF Hideki Matsui NYA |
| 5 | 60th | SP Bartolo Colon LAA |
| 6 | 61st | 3B Troy Glaus Tor |
| 7 | 84th | SP Jason Schmidt SF |
| 8 | 85th | RP Eric Gagne LAD |
| 9 | 108th | SP Dan Haren Oak |
| 10 | 109th | 1B Prince Fielder Mil |
| 11 | 132nd | SP Kelvim Escobar LAA |
| 12 | 133rd | C Jorge Posada NYA |
| 13 | 156th | RP Eddie Guardado Cin |
| 14 | 157th | OF Randy Winn SF |
| 15 | 180th | SP Brad Penny LAD |
| 16 | 181st | 3B Pedro Feliz SF |
| 17 | 204th | SS David Eckstein StL |
| 18 | 205th | C Rod Barajas Tex |
| 19 | 228th | 1B Casey Kotchman LAA |
| 20 | 229th | OF Shawn Green NYN |
| 21 | 252nd | SP Chien-Ming Wang NYA |
| 22 | 253rd | SP David Wells SD |
| 23 | 276th | OF Bill Hall Mil |
| 24 | 277th | RP Chris Reitsma Atl |
| 25 | 300th | 2B Orlando Hudson Ari |
| 26 | 301st | OF Mike Cameron SD |
| 27 | 324th | OF Juan Rivera LAA |
| 28 | 325th | RP Mike Timlin Bos |
| 29 | 348th | C Ryan Doumit Pit |