| Round | Overall | Player |
|---|---|---|
| 1 | 7th | DH Travis Hafner Cle |
| 2 | 18th | 1B Derrek Lee ChN |
| 3 | 31st | OF Matt Holliday Col |
| 4 | 42nd | SP Roy Halladay Tor |
| 5 | 55th | C Brian McCann Atl |
| 6 | 66th | RP Huston Street Oak |
| 7 | 79th | SP Ben Sheets Mil |
| 8 | 90th | SP Rich Harden Oak |
| 9 | 103rd | 2B Dan Uggla Fla |
| 10 | 114th | RP Chris Ray Bal |
| 11 | 127th | OF Rocco Baldelli TB |
| 12 | 138th | 3B Eric Chavez Oak |
| 13 | 151st | SP Anibal Sanchez Fla |
| 14 | 162nd | 3B Edwin Encarnacion Cin |
| 15 | 175th | OF Chris Duncan StL |
| 16 | 186th | SP Chuck James Atl |
| 17 | 199th | 1B Ryan Shealy KC |
| 18 | 210th | OF Corey Patterson Bal |
| 19 | 223rd | SS J.J. Hardy Mil |
| 20 | 234th | SP John Maine NYN |
| 21 | 247th | OF Sammy Sosa Tex |
| 22 | 258th | 2B Marcus Giles SD |
| 23 | 271st | SS Jason Bartlett Min |
| 24 | 282nd | SP Oliver Perez NYN |
| 25 | 295th | SP Noah Lowry SF |
| 26 | 306th | C Gerald Laird Tex |
| 27 | 319th | 1B Scott Thorman Atl |
| 28 | 330th | SP Jon Lester Bos |
| 29 | 343rd | SP Daniel Wheeler TB |