| Round | Overall | Player |
|---|---|---|
| 1 | 5th | 1B Adrian Gonzalez LAD |
| 2 | 20th | SS Jose Reyes Tor |
| 3 | 29th | SP Roy Halladay Phi |
| 4 | 44th | 3B Kevin Youkilis NYA |
| 5 | 53rd | 2B Rickie Weeks Mil |
| 6 | 68th | SP Josh Johnson Tor |
| 7 | 77th | SP Matthew Moore TB |
| 8 | 92nd | C Alex Avila Det |
| 9 | 101st | OF Jason Heyward ATL |
| 10 | 116th | OF Chris Young Oak |
| 11 | 125th | SP Doug Fister Det |
| 12 | 140th | OF Melky Cabrera Tor |
| 13 | 149th | SP Clay Buchholz Bos |
| 14 | 164th | SP Francisco Liriano Pit |
| 15 | 173rd | OF Dexter Fowler Col |
| 16 | 188th | SP Brandon McCarthy Ari |
| 17 | 197th | SP Neftali Feliz Tex |
| 18 | 212th | RP Rafael Betancourt Col |
| 19 | 221st | RP Javy Guerra LAD |
| 20 | 236th | OF Torii Hunter Det |
| 21 | 245th | 3B Ryan Roberts TB |
| 22 | 260th | 2B Gordon Beckham ChA |
| 23 | 269th | SS Rafael Furcal STL |
| 24 | 284th | C Ryan Doumit Min |
| 25 | 293rd | SP Erik Bedard Pit |
| 26 | 308th | SP Aaron Harang LAD |
| 27 | 317th | 1B Aubrey Huff SF |
| 28 | 332nd | DH Travis Hafner Cle |
| 29 | 341st | 1B Adam LaRoche Was |