| Round | Overall | Player |
|---|---|---|
| 1 | 9th | 1B Prince Fielder Tex |
| 2 | 16th | SS Troy Tulowitzki Col |
| 3 | 33rd | OF Jay Bruce Cin |
| 4 | 40th | 2B Ben Zobrist TB |
| 5 | 57th | 1B Freddie Freeman Atl |
| 6 | 64th | SP R.A. Dickey Tor |
| 7 | 81st | OF Carlos Beltran NYA |
| 8 | 88th | SP Brett Anderson Oak |
| 9 | 105th | OF Carl Crawford LAD |
| 10 | 112th | DH David Ortiz Bos |
| 11 | 129th | 3B Chase Headley SD |
| 12 | 136th | 3B Manny Machado Bal |
| 13 | 153rd | SP Doug Fister Was |
| 14 | 160th | 1B Justin Morneau Col |
| 15 | 177th | RP Tom Wilhelmsen Sea |
| 16 | 184th | SP Mike Minor Atl |
| 17 | 201st | SP Mark Buehrle Tor |
| 18 | 208th | SP Josh Beckett LAD |
| 19 | 225th | OF Starling Marte Pit |
| 20 | 232nd | RP Glen Perkins Min |
| 21 | 249th | 2B Pete Kozma StL |
| 22 | 256th | SS Chris Nelson NYA |
| 23 | 273rd | 1B Chris Carter Hou |
| 24 | 280th | RP Steve Cishek Mia |
| 25 | 297th | 3B Luis Cruz LAD |
| 26 | 304th | C Evan Gattis Atl |
| 27 | 321st | C Chris Iannetta LAA |
| 28 | 328th | SP John Lannan Phi |
| 29 | 345th | OF Andy Dirks Det |