| Round | Overall | Player |
|---|---|---|
| 1 | 7th | 1B Ryan Howard Phi |
| 2 | 18th | OF Matt Holliday StL |
| 3 | 31st | SS Jimmy Rollins Phi |
| 4 | 42nd | 2B Brandon Phillips Cin |
| 5 | 55th | OF Curtis Granderson NYA |
| 6 | 66th | SP Johan Santana NYN |
| 7 | 79th | OF Josh Hamilton Tex |
| 8 | 90th | SP Chad Billingsley LAD |
| 9 | 103rd | DH Mike Young Tex |
| 10 | 114th | SP A.J. Burnett NYA |
| 11 | 127th | SP Jered Weaver LAA |
| 12 | 138th | SP Matt Garza ChN |
| 13 | 151st | 3B Adrian Beltre Tex |
| 14 | 162nd | RP Frank Francisco Tex |
| 15 | 175th | OF Conor Jackson Oak |
| 16 | 186th | C Geovany Soto ChN |
| 17 | 199th | OF Garrett Jones Pit |
| 18 | 210th | SP Johnny Cueto Cin |
| 19 | 223rd | 2B Sean Rodriguez TB |
| 20 | 234th | OF Travis Snider Tor |
| 21 | 247th | SP Ted Lilly LAD |
| 22 | 258th | RP Jon Rauch Min |
| 23 | 271st | SP Franklin Morales Col |
| 24 | 282nd | C Kelly Shoppach TB |
| 25 | 295th | SP Jaime Garcia StL |
| 26 | 306th | RP Justin Masterson Cle |
| 27 | 319th | SP Anibal Sanchez Fla |
| 28 | 330th | OF Lastings Milledge Pit |
| 29 | 343rd | 2B Brendan Ryan Sea |