| Round | Overall | Player |
|---|---|---|
| 1 | 2nd | 1B Ryan Howard Phi |
| 2 | 23rd | 1B Lance Berkman Hou |
| 3 | 26th | SS Derek Jeter NYA |
| 4 | 47th | RP Jon Papelbon Bos |
| 5 | 50th | 2B Robinson Cano NYA |
| 6 | 71st | OF Nick Swisher ChA |
| 7 | 74th | RP Mariano Rivera NYA |
| 8 | 95th | OF Torii Hunter LAA |
| 9 | 98th | 3B Mike Lowell Bos |
| 10 | 119th | OF Delmon Young Min |
| 11 | 122nd | SP A.J. Burnett Tor |
| 12 | 143rd | SP Dontrelle Willis Det |
| 13 | 146th | SP Rich Harden ChN |
| 14 | 167th | SP Rich Hill Bal |
| 15 | 170th | SP Derek Lowe Atl |
| 16 | 191st | 3B Alex Gordon KC |
| 17 | 194th | SP Joba Chamberlain NYA |
| 18 | 215th | 1B Billy Butler KC |
| 19 | 218th | C Ramon Hernandez Bal |
| 20 | 239th | OF Luke Scott Bal |
| 21 | 242nd | OF Felix Pie Bal |
| 22 | 263rd | OF Gary Matthews Jr. LAA |
| 23 | 266th | SP Ervin Santana LAA |
| 24 | 287th | SS Yuniesky Betancourt Sea |
| 25 | 290th | SP Jeremy Guthrie Bal |
| 26 | 311th | C Chris Snyder Ari |
| 27 | 314th | SP Mike Mussina NYA |
| 28 | 335th | 2B Jayson Nix Col |
| 29 | 338th | RP Hideki Okajima Bos |