| Round | Overall | Player |
|---|---|---|
| 1 | 9th | SS Miguel Tejada Bal |
| 2 | 16th | OF Jason Bay Pit |
| 3 | 33rd | OF Carlos Beltran NYN |
| 4 | 40th | 1B Lance Berkman Hou |
| 5 | 57th | OF Carlos Lee Hou |
| 6 | 64th | RP Chad Cordero Was |
| 7 | 81st | SP Bartolo Colon LAA |
| 8 | 88th | OF Aubrey Huff Bal |
| 9 | 105th | OF Matt Holliday Col |
| 10 | 112th | RP Jason Isringhausen StL |
| 11 | 129th | SP Cliff Lee Cle |
| 12 | 136th | SP Scott Kazmir TB |
| 13 | 153rd | SP Kevin Millwood Tex |
| 14 | 160th | RP Jose Valverde Ari |
| 15 | 177th | SP Jarrod Washburn Sea |
| 16 | 184th | OF Aaron Rowand Phi |
| 17 | 201st | 2B Placido Polanco Det |
| 18 | 208th | DH Mike Piazza Oak |
| 19 | 225th | 2B Craig Biggio Hou |
| 20 | 232nd | 3B Garrett Atkins Col |
| 21 | 249th | SP Kenny Rogers Det |
| 22 | 256th | 3B Aaron Boone Cle |
| 23 | 273rd | SP Kerry Wood ChN |
| 24 | 280th | 2B Josh Barfield Cle |
| 25 | 297th | C Mike Lieberthal Phi |
| 26 | 304th | OF Bill Hall Mil |
| 27 | 321st | SP Victor Zambrano NYN |
| 28 | 328th | 1B Jeff Bagwell Hou |
| 29 | 345th | 1B Ben Broussard Sea |