| Round | Overall | Player |
|---|---|---|
| 1 | 12th | 2B Ian Kinsler Tex |
| 2 | 13th | SS Jimmy Rollins Phi |
| 3 | 36th | OF Nick Markakis Bal |
| 4 | 37th | 1B Kevin Youkilis Bos |
| 5 | 60th | 1B Carlos Pena TB |
| 6 | 61st | RP Joe Nathan Min |
| 7 | 84th | SP Felix Hernandez Sea |
| 8 | 85th | SP Cliff Lee Sea |
| 9 | 108th | OF Vernon Wells Tor |
| 10 | 109th | SP Scott Kazmir LAA |
| 11 | 132nd | 3B Alex Gordon KC |
| 12 | 133rd | SP Matt Cain SF |
| 13 | 156th | OF Nelson Cruz Tex |
| 14 | 157th | RP Heath Bell SD |
| 15 | 180th | SP David Price TB |
| 16 | 181st | OF Shin-Soo Choo Cle |
| 17 | 204th | C Ben Molina SF |
| 18 | 205th | SP Max Scherzer Det |
| 19 | 228th | RP Matt Lindstrom Hou |
| 20 | 229th | OF Adam Jones Bal |
| 21 | 252nd | SP Jonathan Sanchez SF |
| 22 | 253rd | C John Baker Fla |
| 23 | 276th | SP Todd Wellemeyer StL |
| 24 | 277th | 1B Billy Butler KC |
| 25 | 300th | 2B Aaron Hill Tor |
| 26 | 301st | SP Jordan Zimmermann Was |
| 27 | 324th | 3B Brandon Inge Det |
| 28 | 325th | SS Elvis Andrus Tex |
| 29 | 348th | SP Koji Uehara Bal |