| Round | Overall | Player |
|---|---|---|
| 1 | 2nd | 3B Alex Rodriguez NYA |
| 2 | 23rd | 1B David Ortiz Bos |
| 3 | 26th | SS Derek Jeter NYA |
| 4 | 47th | C Javy Lopez Bal |
| 5 | 50th | SP Roger Clemens Hou |
| 6 | 71st | 2B Mark Loretta SD |
| 7 | 74th | SP Kerry Wood ChN |
| 8 | 95th | RP Octavio Dotel Oak |
| 9 | 98th | RP Guillermo Mota Fla |
| 10 | 119th | SP Chris Carpenter StL |
| 11 | 122nd | OF Brad Wilkerson Was |
| 12 | 143rd | C Joe Mauer Min |
| 13 | 146th | OF Aaron Rowand ChA |
| 14 | 167th | SP Zack Greinke KC |
| 15 | 170th | OF Shannon Stewart Min |
| 16 | 191st | SP Bobby Madritsch Sea |
| 17 | 194th | RP LaTroy Hawkins SF |
| 18 | 215th | OF Jeremy Reed Sea |
| 19 | 218th | SS Jack Wilson Pit |
| 20 | 239th | 1B J.T. Snow SF |
| 21 | 242nd | OF Nick Swisher Oak |
| 22 | 263rd | SP Kenny Rogers Tex |
| 23 | 266th | SP Victor Zambrano NYN |
| 24 | 287th | SP Ted Lilly Tor |
| 25 | 290th | 3B Edgardo Alfonzo SF |
| 26 | 311th | 2B Ron Belliard Cle |
| 27 | 314th | 2B Chris Burke Hou |
| 28 | 335th | SP Luke Hudson Cin |
| 29 | 338th | OF Craig Monroe Det |