| Round | Overall | Player |
|---|---|---|
| 1 | 1st | 3B Alex Rodriguez NYA |
| 2 | 24th | SP Josh Beckett Bos |
| 3 | 25th | OF Adam Dunn Ari |
| 4 | 48th | SP Erik Bedard Sea |
| 5 | 49th | 1B Derrek Lee ChN |
| 6 | 72nd | SP John Lackey LAA |
| 7 | 73rd | 2B Dan Uggla Fla |
| 8 | 96th | OF Jeff Francoeur Atl |
| 9 | 97th | RP Jose Valverde Hou |
| 10 | 120th | OF Chris Young Ari |
| 11 | 121st | SP Matt Cain SF |
| 12 | 144th | SS Khalil Greene SD |
| 13 | 145th | RP Joe Borowski Cle |
| 14 | 168th | C Kenji Johjima Sea |
| 15 | 169th | SP Kelvim Escobar LAA |
| 16 | 192nd | 3B Evan Longoria TB |
| 17 | 193rd | RP Jason Isringhausen StL |
| 18 | 216th | C Carlos Ruiz Phi |
| 19 | 217th | 1B Joey Votto Cin |
| 20 | 240th | OF Adam Jones Bal |
| 21 | 241st | 2B Aaron Hill Tor |
| 22 | 264th | OF Cameron Maybin Fla |
| 23 | 265th | SP Scott Olsen Was |
| 24 | 288th | OF Michael Bourn Hou |
| 25 | 289th | OF Jay Bruce Cin |
| 26 | 312th | 3B Andy LaRoche Pit |
| 27 | 313th | SP Chuck James Atl |
| 28 | 336th | SP Jason Schmidt LAD |
| 29 | 337th | 3B Pedro Feliz Phi |