| Round | Overall | Player |
|---|---|---|
| 1 | 7th | 1B Albert Pujols StL |
| 2 | 18th | OF Carlos Beltran NYN |
| 3 | 31st | OF Alexis Rios Tor |
| 4 | 42nd | 1B Derrek Lee ChN |
| 5 | 55th | 3B Garrett Atkins Col |
| 6 | 66th | 3B Mike Young Tex |
| 7 | 79th | OF Jason Bay Bos |
| 8 | 90th | OF Bobby Abreu NYA |
| 9 | 103rd | RP Huston Street Oak |
| 10 | 114th | SP Tim Hudson Atl |
| 11 | 127th | SP Chris Young SD |
| 12 | 138th | RP Trevor Hoffman Mil |
| 13 | 151st | SP James Shields TB |
| 14 | 162nd | SP Rich Harden ChN |
| 15 | 175th | SS Edgar Renteria Det |
| 16 | 186th | 3B Mark Reynolds Ari |
| 17 | 199th | SP Matt Garza TB |
| 18 | 210th | 2B Dustin Pedroia Bos |
| 19 | 223rd | C Ramon Hernandez Bal |
| 20 | 234th | 2B Jeff Kent LAD |
| 21 | 247th | OF Austin Kearns Was |
| 22 | 258th | DH Frank Thomas Oak |
| 23 | 271st | SP Bartolo Colon ChA |
| 24 | 282nd | SP Chris Capuano Mil |
| 25 | 295th | SP Micah Owings Ari |
| 26 | 306th | SP Zack Greinke KC |
| 27 | 319th | SP George Sherrill Sea |
| 28 | 330th | 3B Brandon Wood LAA |
| 29 | 343rd | C Carlos Ruiz Phi |