| Round | Overall | Player |
|---|---|---|
| 1 | 10th | 1B Miguel Cabrera Det |
| 2 | 15th | SP Tim Lincecum SF |
| 3 | 34th | OF Justin Upton Ari |
| 4 | 39th | 2B Robinson Cano NYA |
| 5 | 58th | RP Jonathan Broxton LAD |
| 6 | 63rd | OF Josh Hamilton Tex |
| 7 | 82nd | RP Joakim Soria KC |
| 8 | 87th | OF Carlos Lee Hou |
| 9 | 106th | SP Cole Hamels Phi |
| 10 | 111th | RP Andrew Bailey Oak |
| 11 | 130th | SP A.J. Burnett NYA |
| 12 | 135th | OF Shane Victorino Phi |
| 13 | 154th | SS Asdrubal Cabrera Cle |
| 14 | 159th | SP Brett Anderson Oak |
| 15 | 178th | SP Brandon Webb Tex |
| 16 | 183rd | 3B Miguel Tejada SD |
| 17 | 202nd | DH Vladimir Guerrero Tex |
| 18 | 207th | 3B Placido Polanco Phi |
| 19 | 226th | 1B James Loney LAD |
| 20 | 231st | C A.J. Pierzynski ChA |
| 21 | 250th | SP Jason Frasor Tor |
| 22 | 255th | 3B David Freese StL |
| 23 | 274th | SP Barry Zito SF |
| 24 | 279th | 2B Clint Barmes Col |
| 25 | 298th | DH Travis Hafner Cle |
| 26 | 303rd | C John Buck Fla |
| 27 | 322nd | OF Drew Stubbs Cin |
| 28 | 327th | C John Baker Fla |
| 29 | 346th | SP John Maine NYN |