| Round | Overall | Player |
|---|---|---|
| 1 | 3rd | SS Troy Tulowitzki Col |
| 2 | 22nd | 3B Kevin Youkilis Bos |
| 3 | 27th | DH Adam Dunn ChA |
| 4 | 46th | SP Clayton Kershaw LAD |
| 5 | 51st | DH Victor Martinez Det |
| 6 | 70th | OF Hunter Pence Phi |
| 7 | 75th | SP Chris Carpenter StL |
| 8 | 94th | RP Mariano Rivera NYA |
| 9 | 99th | 2B Gordon Beckham ChA |
| 10 | 118th | SP Jeremy Hellickson TB |
| 11 | 123rd | C Geovany Soto ChN |
| 12 | 142nd | SP Brandon Morrow Tor |
| 13 | 147th | SP Roberto Hernandez Cle |
| 14 | 166th | OF Torii Hunter LAA |
| 15 | 171st | 3B Scott Rolen Cin |
| 16 | 190th | SP Brett Cecil Tor |
| 17 | 195th | DH Jorge Posada NYA |
| 18 | 214th | RP Aroldis Chapman Cin |
| 19 | 219th | 1B Mitch Moreland Tex |
| 20 | 238th | OF Fred Lewis Cin |
| 21 | 243rd | SP Andy Pettitte NYA |
| 22 | 262nd | RP Rafael Soriano NYA |
| 23 | 267th | C Carlos Ruiz Phi |
| 24 | 286th | SP Barry Enright Ari |
| 25 | 291st | RP Jonny Venters Atl |
| 26 | 310th | SP Charlie Morton Pit |
| 27 | 315th | SP Hong-Chih Kuo LAD |
| 28 | 334th | SP Brandon Webb Tex |
| 29 | 339th | RP Alexi Ogando Tex |