| Round | Overall | Player |
|---|---|---|
| 1 | 9th | DH David Ortiz Bos |
| 2 | 16th | OF Ryan Braun Mil |
| 3 | 33rd | SP Roy Halladay Tor |
| 4 | 40th | SP Cole Hamels Phi |
| 5 | 57th | RP Francisco Rodriguez LAA |
| 6 | 64th | SP Roberto Hernandez Cle |
| 7 | 81st | RP Billy Wagner NYN |
| 8 | 88th | OF Josh Hamilton Tex |
| 9 | 105th | OF Eric Byrnes Ari |
| 10 | 112th | 3B Adrian Beltre Sea |
| 11 | 129th | 2B Kelly Johnson Atl |
| 12 | 136th | SP Oliver Perez NYN |
| 13 | 153rd | SS Edgar Renteria Det |
| 14 | 160th | C Geovany Soto ChN |
| 15 | 177th | SP Jon Lester Bos |
| 16 | 184th | 1B Kevin Youkilis Bos |
| 17 | 201st | SS J.J. Hardy Mil |
| 18 | 208th | OF Austin Kearns Was |
| 19 | 225th | OF Lastings Milledge Was |
| 20 | 232nd | OF Melky Cabrera NYA |
| 21 | 249th | 2B Tadahito Iguchi SD |
| 22 | 256th | SP Brian Bannister KC |
| 23 | 273rd | C J.R. Towles Hou |
| 24 | 280th | 3B Jose Bautista Pit |
| 25 | 297th | OF Jack Cust Oak |
| 26 | 304th | RP Miguel Batista Sea |
| 27 | 321st | SP Kevin Gregg Fla |
| 28 | 328th | SP Randy Wolf LAD |
| 29 | 345th | SP George Sherrill Sea |