| Round | Overall | Player |
|---|---|---|
| 1 | 2nd | 3B David Wright NYN |
| 2 | 23rd | 1B Prince Fielder Mil |
| 3 | 26th | 2B Brandon Phillips Cin |
| 4 | 47th | OF Nate McLouth Atl |
| 5 | 50th | OF Carl Crawford TB |
| 6 | 71st | C Russell Martin LAD |
| 7 | 74th | SP Edison Volquez Cin |
| 8 | 95th | RP Joakim Soria KC |
| 9 | 98th | SP Chien-Ming Wang NYA |
| 10 | 119th | RP Kerry Wood Cle |
| 11 | 122nd | 3B Miguel Tejada Bal |
| 12 | 143rd | SP Scott Baker Min |
| 13 | 146th | OF Jacoby Ellsbury Bos |
| 14 | 167th | SP Jair Jurrjens Atl |
| 15 | 170th | SP Jon Garland SD |
| 16 | 191st | SP Jeremy Guthrie Bal |
| 17 | 194th | C Kelly Shoppach Cle |
| 18 | 215th | SP Oliver Perez NYN |
| 19 | 218th | 2B Jed Lowrie Bos |
| 20 | 239th | 3B Mike Lowell Bos |
| 21 | 242nd | OF Xavier Nady ChN |
| 22 | 263rd | RP Huston Street Col |
| 23 | 266th | SP John Smoltz Hou |
| 24 | 287th | OF Ken Griffey Jr Sea |
| 25 | 290th | 1B Lyle Overbay Tor |
| 26 | 311th | 2B Freddy Sanchez SF |
| 27 | 314th | OF Nick Swisher NYA |
| 28 | 335th | SP Anthony Reyes Cle |
| 29 | 338th | SP Carl Pavano Min |