| Round | Overall | Player |
|---|---|---|
| 1 | 2nd | 1B Albert Pujols StL |
| 2 | 23rd | 3B Aramis Ramirez ChN |
| 3 | 26th | SS Jhonny Peralta Cle |
| 4 | 47th | RP Billy Wagner NYN |
| 5 | 50th | RP Brad Lidge Hou |
| 6 | 71st | SP John Smoltz Atl |
| 7 | 74th | 3B Scott Rolen StL |
| 8 | 95th | SP John Patterson Was |
| 9 | 98th | OF Jonny Gomes TB |
| 10 | 119th | OF Brad Wilkerson Tex |
| 11 | 122nd | 1B Chris Shelton Det |
| 12 | 143rd | RP Derrick Turnbow Mil |
| 13 | 146th | RP Tom Gordon Phi |
| 14 | 167th | OF Preston Wilson StL |
| 15 | 170th | RP Todd Jones Det |
| 16 | 191st | 2B Mark Ellis Oak |
| 17 | 194th | SS Carlos Guillen Det |
| 18 | 215th | SP Chien-Ming Wang NYA |
| 19 | 218th | SP Jae Weong Seo TB |
| 20 | 239th | SP Tom Glavine NYN |
| 21 | 242nd | C A.J. Pierzynski ChA |
| 22 | 263rd | SP Aaron Heilman NYN |
| 23 | 266th | SP Jon Papelbon Bos |
| 24 | 287th | C Jason LaRue KC |
| 25 | 290th | C Javier Valentin Cin |
| 26 | 311th | OF Nick Swisher Oak |
| 27 | 314th | 1B Conor Jackson Ari |
| 28 | 335th | 2B Todd Walker SD |
| 29 | 338th | SP Oscar Villarreal Atl |