| Round | Overall | Player |
|---|---|---|
| 1 | 2nd | 1B Albert Pujols StL |
| 2 | 23rd | 3B Morgan Ensberg Hou |
| 3 | 26th | SS Derek Jeter NYA |
| 4 | 47th | RP Mariano Rivera NYA |
| 5 | 50th | OF Carl Crawford TB |
| 6 | 71st | SP Andy Pettitte Hou |
| 7 | 74th | OF Johnny Damon NYA |
| 8 | 95th | C Jason Varitek Bos |
| 9 | 98th | SP Kevin Millwood Tex |
| 10 | 119th | SP Carlos Silva Min |
| 11 | 122nd | SP Dan Haren Oak |
| 12 | 143rd | OF J.D. Drew LAD |
| 13 | 146th | 2B Mark Ellis Oak |
| 14 | 167th | SP Joe Blanton Oak |
| 15 | 170th | OF Mike Cameron SD |
| 16 | 191st | OF Moises Alou SF |
| 17 | 194th | SP Paul Byrd Cle |
| 18 | 215th | SP Greg Maddux SD |
| 19 | 218th | 1B Casey Kotchman LAA |
| 20 | 239th | SP Tom Glavine NYN |
| 21 | 242nd | 3B Ryan Zimmerman Was |
| 22 | 263rd | SP Josh Towers Tor |
| 23 | 266th | SS David Eckstein StL |
| 24 | 287th | C Jason LaRue KC |
| 25 | 290th | OF Brady Clark Mil |
| 26 | 311th | OF Jacque Jones ChN |
| 27 | 314th | OF Xavier Nady Pit |
| 28 | 335th | 2B Adam Kennedy LAA |
| 29 | 338th | SP Cory Lidle NYA |