| Round | Overall | Player |
|---|---|---|
| 1 | 3rd | 1B Albert Pujols StL |
| 2 | 22nd | SP Johan Santana NYN |
| 3 | 27th | OF Melvin Upton TB |
| 4 | 46th | SP Jon Lester Bos |
| 5 | 51st | C Brian McCann Atl |
| 6 | 70th | RP Francisco Rodriguez NYN |
| 7 | 75th | 2B Robinson Cano NYA |
| 8 | 94th | OF Hunter Pence Hou |
| 9 | 99th | RP Jose Valverde Det |
| 10 | 118th | OF Jacoby Ellsbury Bos |
| 11 | 123rd | SP Derek Lowe Atl |
| 12 | 142nd | 3B Adrian Beltre Bos |
| 13 | 147th | SP Brett Myers Hou |
| 14 | 166th | SP Joe Saunders LAA |
| 15 | 171st | OF Shin-Soo Choo Cle |
| 16 | 190th | SP Oliver Perez NYN |
| 17 | 195th | SP Jonathan Sanchez SF |
| 18 | 214th | 1B James Loney LAD |
| 19 | 219th | SS Ryan Theriot ChN |
| 20 | 238th | SP Armando Galarraga Det |
| 21 | 243rd | OF Jeff Francoeur NYN |
| 22 | 262nd | SS Cristian Guzman Was |
| 23 | 267th | 2B Kazuo Matsui Hou |
| 24 | 286th | SP Wandy Rodriguez Hou |
| 25 | 291st | 3B Brandon Inge Det |
| 26 | 310th | C Taylor Teagarden Tex |
| 27 | 315th | SP Jose Contreras Phi |
| 28 | 334th | OF Ken Griffey Jr Sea |
| 29 | 339th | OF Adam Lind Tor |