| Round | Overall | Player |
|---|---|---|
| 1 | 2nd | SS Hanley Ramirez Fla |
| 2 | 23rd | 3B Aramis Ramirez ChN |
| 3 | 26th | SP Roy Halladay Tor |
| 4 | 47th | OF Carlos Quentin ChA |
| 5 | 50th | SP John Lackey Bos |
| 6 | 71st | RP Joakim Soria KC |
| 7 | 74th | OF Jason Bay NYN |
| 8 | 95th | 1B Joey Votto Cin |
| 9 | 98th | C Mike Napoli LAA |
| 10 | 119th | RP Kerry Wood Cle |
| 11 | 122nd | SP Josh Johnson Fla |
| 12 | 143rd | OF Mark DeRosa SF |
| 13 | 146th | SP Matt Garza TB |
| 14 | 167th | 1B James Loney LAD |
| 15 | 170th | SP Hiroki Kuroda LAD |
| 16 | 191st | C Kelly Shoppach Cle |
| 17 | 194th | SP Chris Volstad Fla |
| 18 | 215th | OF Johnny Damon NYA |
| 19 | 218th | SP John Maine NYN |
| 20 | 239th | OF Delmon Young Min |
| 21 | 242nd | 2B Alexi Casilla Min |
| 22 | 263rd | OF Nick Swisher NYA |
| 23 | 266th | 3B Casey Blake LAD |
| 24 | 287th | OF Adam Lind Tor |
| 25 | 290th | SP Brad Penny StL |
| 26 | 311th | SS Cristian Guzman Was |
| 27 | 314th | SP Vicente Padilla LAD |
| 28 | 335th | C Taylor Teagarden Tex |
| 29 | 338th | 2B Mike Fontenot ChN |