| Round | Overall | Player |
|---|---|---|
| 1 | 7th | 1B Miguel Cabrera Det |
| 2 | 18th | OF Alfonso Soriano ChN |
| 3 | 31st | OF Carlos Beltran NYN |
| 4 | 42nd | 1B Adrian Gonzalez SD |
| 5 | 55th | SP Cole Hamels Phi |
| 6 | 66th | OF Nick Markakis Bal |
| 7 | 79th | 2B Dan Uggla Fla |
| 8 | 90th | SS Rafael Furcal LAD |
| 9 | 103rd | OF Delmon Young Min |
| 10 | 114th | SP Tim Lincecum Hou |
| 11 | 127th | 1B James Loney LAD |
| 12 | 138th | SP Matt Cain SF |
| 13 | 151st | 3B Troy Glaus StL |
| 14 | 162nd | SS Jhonny Peralta Cle |
| 15 | 175th | 1B Ryan Garko Cle |
| 16 | 186th | SP Matt Capps Pit |
| 17 | 199th | RP Brian Wilson SF |
| 18 | 210th | SP Jon Garland Ari |
| 19 | 223rd | SP Ubaldo Jimenez Col |
| 20 | 234th | C Ramon Hernandez Bal |
| 21 | 247th | SP Barry Zito SF |
| 22 | 258th | OF Adam Jones Bal |
| 23 | 271st | C Yorvit Torrealba Col |
| 24 | 282nd | 2B Brendan Harris Min |
| 25 | 295th | OF Chase Headley SD |
| 26 | 306th | SP Braden Looper StL |
| 27 | 319th | SP Cliff Lee Cle |
| 28 | 330th | SP Kevin Correia SF |
| 29 | 343rd | SP Gavin Floyd ChA |