| Round | Overall | Player |
|---|---|---|
| 1 | 10th | SS Jose Reyes NYN |
| 2 | 15th | 3B David Wright NYN |
| 3 | 34th | 1B Justin Morneau Min |
| 4 | 39th | SP Carlos Zambrano ChN |
| 5 | 58th | RP Billy Wagner NYN |
| 6 | 63rd | RP B.J. Ryan Tor |
| 7 | 82nd | OF Delmon Young Min |
| 8 | 87th | 2B Brian Roberts Bal |
| 9 | 106th | OF Nick Swisher ChA |
| 10 | 111th | SP Dan Haren Ari |
| 11 | 130th | SP Ervin Santana LAA |
| 12 | 135th | DH Frank Thomas Tor |
| 13 | 154th | SP Brad Penny LAD |
| 14 | 159th | OF Raul Ibanez Sea |
| 15 | 178th | C Russell Martin LAD |
| 16 | 183rd | SP Chris Capuano Mil |
| 17 | 202nd | SS Julio Lugo Bos |
| 18 | 207th | SP Scott Olsen Fla |
| 19 | 226th | SP Brandon McCarthy Tex |
| 20 | 231st | RP Clay Hensley SD |
| 21 | 250th | C Chris Iannetta Col |
| 22 | 255th | 3B Casey Blake Cle |
| 23 | 274th | OF Eric Byrnes Ari |
| 24 | 279th | 3B Kevin Kouzmanoff SD |
| 25 | 298th | SP Esteban Loaiza LAD |
| 26 | 303rd | OF Jose Guillen KC |
| 27 | 322nd | OF Josh Hamilton Tex |
| 28 | 327th | SP Adam Miller Cle |
| 29 | 346th | 2B Mark DeRosa ChN |