| Round | Overall | Player |
|---|---|---|
| 1 | 1st | 1B Albert Pujols StL |
| 2 | 24th | 1B Prince Fielder Mil |
| 3 | 25th | 2B Brandon Phillips Cin |
| 4 | 48th | 3B Chipper Jones Atl |
| 5 | 49th | SP Roy Oswalt Hou |
| 6 | 72nd | SS Derek Jeter NYA |
| 7 | 73rd | SP Felix Hernandez Sea |
| 8 | 96th | OF Bobby Abreu LAA |
| 9 | 97th | SP Carlos Zambrano ChN |
| 10 | 120th | OF Milton Bradley Sea |
| 11 | 121st | C Chris Iannetta Col |
| 12 | 144th | RP Jonathan Broxton LAD |
| 13 | 145th | OF Justin Upton Ari |
| 14 | 168th | SP Roberto Hernandez Cle |
| 15 | 169th | RP Chad Qualls Ari |
| 16 | 192nd | SP Jeremy Guthrie Bal |
| 17 | 193rd | OF Elijah Dukes Was |
| 18 | 216th | 2B Howie Kendrick LAA |
| 19 | 217th | 3B Kevin Kouzmanoff Oak |
| 20 | 240th | SP Armando Galarraga Det |
| 21 | 241st | SS Khalil Greene Tex |
| 22 | 264th | DH Hideki Matsui LAA |
| 23 | 265th | SP Clay Buchholz Bos |
| 24 | 288th | 1B Ryan Garko SF |
| 25 | 289th | DH Jack Cust Oak |
| 26 | 312th | RP Manuel Corpas Col |
| 27 | 313th | SP Philip Hughes NYA |
| 28 | 336th | C Nick Hundley SD |
| 29 | 337th | SP Jose Contreras Phi |