| Round | Overall | Player |
|---|---|---|
| 1 | 7th | 1B Ryan Howard Phi |
| 2 | 18th | OF Vladimir Guerrero LAA |
| 3 | 31st | OF Melvin Upton TB |
| 4 | 42nd | SP Erik Bedard Sea |
| 5 | 55th | SP Roy Oswalt Hou |
| 6 | 66th | SP John Lackey LAA |
| 7 | 79th | OF Jason Bay Bos |
| 8 | 90th | SP Ben Sheets Mil |
| 9 | 103rd | DH Jim Thome ChA |
| 10 | 114th | SP Chien-Ming Wang NYA |
| 11 | 127th | 3B Troy Glaus StL |
| 12 | 138th | SS J.J. Hardy Mil |
| 13 | 151st | SP Adam Wainwright StL |
| 14 | 162nd | OF Jeremy Hermida Fla |
| 15 | 175th | 3B Edwin Encarnacion Cin |
| 16 | 186th | 2B Akinori Iwamura TB |
| 17 | 199th | SP Rich Harden ChN |
| 18 | 210th | OF Chris Duncan StL |
| 19 | 223rd | SP Jake Westbrook Cle |
| 20 | 234th | 1B Richie Sexson Sea |
| 21 | 247th | C J.R. Towles Hou |
| 22 | 258th | RP Manuel Corpas Col |
| 23 | 271st | OF Mike Cameron Mil |
| 24 | 282nd | 2B Brendan Harris Min |
| 25 | 295th | C Yorvit Torrealba Col |
| 26 | 306th | RP Carlos Marmol ChN |
| 27 | 319th | SP Tim Wakefield Bos |
| 28 | 330th | SS Jack Wilson Pit |
| 29 | 343rd | OF Matt LaPorta Cle |