| Round | Overall | Player |
|---|---|---|
| 1 | 2nd | 3B Alex Rodriguez NYA |
| 2 | 23rd | OF Jason Bay Pit |
| 3 | 26th | C Brian McCann Atl |
| 4 | 47th | RP Billy Wagner NYN |
| 5 | 50th | SP Jake Peavy SD |
| 6 | 71st | RP Chris Ray Bal |
| 7 | 74th | 1B Todd Helton Col |
| 8 | 95th | OF Magglio Ordonez Det |
| 9 | 98th | SP Josh Beckett Bos |
| 10 | 119th | SP Randy Johnson Ari |
| 11 | 122nd | 2B Josh Barfield Cle |
| 12 | 143rd | OF Austin Kearns Was |
| 13 | 146th | OF Jonny Gomes TB |
| 14 | 167th | SP Zach Duke Pit |
| 15 | 170th | SP Jon Garland LAA |
| 16 | 191st | 2B Freddy Sanchez Pit |
| 17 | 194th | RP Salomon Torres Mil |
| 18 | 215th | 3B Brandon Inge Det |
| 19 | 218th | SS Troy Tulowitzki Col |
| 20 | 239th | OF Moises Alou NYN |
| 21 | 242nd | SP Cliff Lee Cle |
| 22 | 263rd | 1B Sean Casey Det |
| 23 | 266th | C Paul Lo Duca Was |
| 24 | 287th | SP Jarrod Washburn Sea |
| 25 | 290th | SP Jon Lester Bos |
| 26 | 311th | OF Curtis Granderson Det |
| 27 | 314th | SS Yuniesky Betancourt Sea |
| 28 | 335th | 2B Dustin Pedroia Bos |