| Round | Overall | Player |
|---|---|---|
| 1 | 12th | SP Roy Halladay Phi |
| 2 | 13th | SS Troy Tulowitzki Col |
| 3 | 36th | 2B Dustin Pedroia Bos |
| 4 | 37th | SP Adam Wainwright StL |
| 5 | 60th | 1B Adam Dunn ChA |
| 6 | 61st | SP Cole Hamels Phi |
| 7 | 84th | OF Jay Bruce Cin |
| 8 | 85th | SP Ubaldo Jimenez Col |
| 9 | 108th | OF Hunter Pence Hou |
| 10 | 109th | RP Rafael Soriano TB |
| 11 | 132nd | SP James Shields TB |
| 12 | 133rd | OF Ryan Ludwick SD |
| 13 | 156th | 3B Jorge Cantu Tex |
| 14 | 157th | 1B Adam LaRoche Was |
| 15 | 180th | RP Frank Francisco Tex |
| 16 | 181st | OF Travis Snider Tor |
| 17 | 204th | C Kurt Suzuki Oak |
| 18 | 205th | RP Leo Nunez Fla |
| 19 | 228th | SP Aroldis Chapman Cin |
| 20 | 229th | 3B Martin Prado Atl |
| 21 | 252nd | SP Justin Duchscherer Oak |
| 22 | 253rd | 1B Paul Konerko ChA |
| 23 | 276th | OF Cody Ross Fla |
| 24 | 277th | SP Vicente Padilla LAD |
| 25 | 300th | 3B Jose Bautista Tor |
| 26 | 301st | SP Matt Guerrier Min |