| Round | Overall | Player |
|---|---|---|
| 1 | 1st | 1B Albert Pujols StL |
| 2 | 24th | SS Jimmy Rollins Phi |
| 3 | 25th | C Brian McCann Atl |
| 4 | 48th | 2B Aaron Hill Tor |
| 5 | 49th | OF Nick Markakis Bal |
| 6 | 72nd | SP John Lackey Bos |
| 7 | 73rd | SP Tommy Hanson Atl |
| 8 | 96th | SP Rick Porcello Det |
| 9 | 97th | OF Carlos Lee Hou |
| 10 | 120th | SP James Shields TB |
| 11 | 121st | OF Denard Span Min |
| 12 | 144th | 1B Brad Hawpe SD |
| 13 | 145th | RP Carlos Marmol ChN |
| 14 | 168th | RP Chad Qualls TB |
| 15 | 169th | RP Bobby Jenks Bos |
| 16 | 192nd | 3B Miguel Tejada SD |
| 17 | 193rd | SP Brian Matusz Bal |
| 18 | 216th | SP Randy Wells ChN |
| 19 | 217th | SS Jhonny Peralta Det |
| 20 | 240th | OF Corey Hart Mil |
| 21 | 241st | OF Franklin Gutierrez Sea |
| 22 | 264th | 3B Brandon Inge Det |
| 23 | 265th | RP Justin Masterson Cle |
| 24 | 288th | 1B Aubrey Huff SF |
| 25 | 289th | 2B Orlando Hudson Min |
| 26 | 312th | OF Milton Bradley Sea |
| 27 | 313th | C Ramon Hernandez Cin |
| 28 | 336th | SP Matt Thornton ChA |
| 29 | 337th | SS Cristian Guzman Tex |