| Round | Overall | Player |
|---|---|---|
| 1 | 9th | 1B Ryan Howard Phi |
| 2 | 16th | 2B Brandon Phillips Cin |
| 3 | 33rd | 3B Aramis Ramirez ChN |
| 4 | 40th | RP Jon Papelbon Bos |
| 5 | 57th | SP Roy Oswalt Hou |
| 6 | 64th | SP Roy Halladay Tor |
| 7 | 81st | OF Hideki Matsui NYA |
| 8 | 88th | OF Chris Young Ari |
| 9 | 105th | 3B Alex Gordon KC |
| 10 | 112th | 1B Jarrod Saltalamacchia Tex |
| 11 | 129th | RP Manuel Corpas Col |
| 12 | 136th | SS Rafael Furcal LAD |
| 13 | 153rd | SP Matt Cain SF |
| 14 | 160th | OF Jay Bruce Cin |
| 15 | 177th | OF Jacoby Ellsbury Bos |
| 16 | 184th | OF Kosuke Fukudome ChN |
| 17 | 201st | 1B Billy Butler KC |
| 18 | 208th | SP Ian Kennedy NYA |
| 19 | 225th | C J.R. Towles Hou |
| 20 | 232nd | 2B Akinori Iwamura TB |
| 21 | 249th | SP Franklin Morales Col |
| 22 | 256th | SP Mike Mussina NYA |
| 23 | 273rd | SP Manny Parra Mil |
| 24 | 280th | SP Hiroki Kuroda LAD |
| 25 | 297th | OF Franklin Gutierrez Cle |
| 26 | 304th | SP Tim Wakefield Bos |
| 27 | 321st | SP Curt Schilling Bos |
| 28 | 328th | SP Michael Pelfrey NYN |
| 29 | 345th | SS Yuniesky Betancourt Sea |