| Round | Overall | Player |
|---|---|---|
| 1 | 3rd | 2B Chase Utley Phi |
| 2 | 22nd | OF Matt Holliday Col |
| 3 | 27th | SP Brandon Webb Ari |
| 4 | 46th | SP Roy Halladay Tor |
| 5 | 51st | SP Jake Peavy SD |
| 6 | 70th | OF Delmon Young Min |
| 7 | 75th | SP Felix Hernandez Sea |
| 8 | 94th | SP Josh Beckett Bos |
| 9 | 99th | 3B Adrian Beltre Sea |
| 10 | 118th | SS Stephen Drew Ari |
| 11 | 123rd | 2B Howie Kendrick LAA |
| 12 | 142nd | OF Rocco Baldelli TB |
| 13 | 147th | 1B Conor Jackson Ari |
| 14 | 166th | OF Chris Young Ari |
| 15 | 171st | C Russell Martin LAD |
| 16 | 190th | 3B Edwin Encarnacion Cin |
| 17 | 195th | SP Joe Blanton Oak |
| 18 | 214th | SS Troy Tulowitzki Col |
| 19 | 219th | OF Chris Duncan StL |
| 20 | 238th | 1B Ryan Shealy KC |
| 21 | 243rd | 3B Kevin Kouzmanoff SD |
| 22 | 262nd | OF Corey Hart Mil |
| 23 | 267th | SP Michael Pelfrey NYN |
| 24 | 286th | 3B Casey Blake Cle |
| 25 | 291st | SP Philip Hughes NYA |
| 26 | 310th | C Miguel Montero Ari |
| 27 | 315th | OF Matt Murton ChN |
| 28 | 334th | OF Lastings Milledge Was |
| 29 | 339th | SP Adam Loewen Bal |