| Round | Overall | Player |
|---|---|---|
| 1 | 11th | OF Carl Crawford Bos |
| 2 | 14th | SS Jose Reyes NYN |
| 3 | 35th | SP Felix Hernandez Sea |
| 4 | 38th | 3B Chone Figgins Sea |
| 5 | 59th | 1B Billy Butler KC |
| 6 | 62nd | C Russell Martin NYA |
| 7 | 83rd | SP Chad Billingsley LAD |
| 8 | 86th | OF Shin-Soo Choo Cle |
| 9 | 107th | OF Hunter Pence Hou |
| 10 | 110th | 2B Jose Lopez Col |
| 11 | 131st | RP Bobby Jenks Bos |
| 12 | 134th | 1B James Loney LAD |
| 13 | 155th | C Geovany Soto ChN |
| 14 | 158th | SP David Price TB |
| 15 | 179th | SP Ryan Dempster ChN |
| 16 | 182nd | SS Ryan Theriot STL |
| 17 | 203rd | RP Mike Gonzalez Bal |
| 18 | 206th | OF Mark DeRosa SF |
| 19 | 227th | 2B Akinori Iwamura Pit |
| 20 | 230th | SP Brian Bannister KC |
| 21 | 251st | SP Andy Pettitte NYA |
| 22 | 254th | OF Ken Griffey Jr Sea |
| 23 | 275th | 3B Garrett Atkins Pit |
| 24 | 278th | SP Daisuke Matsuzaka Bos |
| 25 | 299th | SP Vicente Padilla LAD |
| 26 | 302nd | OF Marlon Byrd ChN |
| 27 | 323rd | OF Jonny Gomes Cin |
| 28 | 326th | SP Michael Wuertz Oak |
| 29 | 347th | DH Jack Cust Sea |