| Round | Overall | Player |
|---|---|---|
| 1 | 8th | SS Jose Reyes NYN |
| 2 | 17th | OF Carl Crawford TB |
| 3 | 32nd | SP Cole Hamels Phi |
| 4 | 41st | SP C.C. Sabathia Mil |
| 5 | 56th | SP Carlos Zambrano ChN |
| 6 | 65th | 3B Chone Figgins LAA |
| 7 | 80th | OF Vernon Wells Tor |
| 8 | 89th | OF Brad Hawpe Col |
| 9 | 104th | SP Brad Penny LAD |
| 10 | 113th | 1B James Loney LAD |
| 11 | 128th | SP Tim Lincecum Hou |
| 12 | 137th | 2B Placido Polanco Det |
| 13 | 152nd | 1B Adam LaRoche Pit |
| 14 | 161st | RP Huston Street Oak |
| 15 | 176th | SP Tom Gorzelanny Pit |
| 16 | 185th | OF Gary Matthews Jr. LAA |
| 17 | 200th | C Jason Varitek Bos |
| 18 | 209th | SP Ubaldo Jimenez Col |
| 19 | 224th | SS Bobby Crosby Oak |
| 20 | 233rd | C Mike Napoli LAA |
| 21 | 248th | RP Chad Cordero Was |
| 22 | 257th | 1B Dan Johnson Oak |
| 23 | 272nd | RP Joakim Soria KC |
| 24 | 281st | 3B Jose Bautista Pit |
| 25 | 296th | OF Jonny Gomes Cin |
| 26 | 305th | OF Mark Teahen KC |
| 27 | 320th | SP Chad Gaudin ChN |
| 28 | 329th | OF Elijah Dukes Was |
| 29 | 344th | OF Carlos Gonzalez OAK |