| Round | Overall | Player |
|---|---|---|
| 1 | 12th | OF Carlos Gonzalez Col |
| 2 | 13th | 1B Prince Fielder Mil |
| 3 | 36th | OF Nelson Cruz Tex |
| 4 | 37th | 1B Justin Morneau Min |
| 5 | 60th | 3B Mark Reynolds Bal |
| 6 | 61st | 2B Chase Utley Phi |
| 7 | 84th | RP Joakim Soria KC |
| 8 | 85th | RP Heath Bell Fla |
| 9 | 108th | SS Alexei Ramirez ChA |
| 10 | 109th | SP Tim Hudson Atl |
| 11 | 132nd | SP John Lackey Bos |
| 12 | 133rd | SP Ted Lilly LAD |
| 13 | 156th | OF Vernon Wells LAA |
| 14 | 157th | 2B Brian Roberts Bal |
| 15 | 180th | C Miguel Montero Ari |
| 16 | 181st | SP Brandon Morrow Tor |
| 17 | 204th | 2B Howie Kendrick LAA |
| 18 | 205th | SP Brian Matusz Bal |
| 19 | 228th | SP Hiroki Kuroda NYA |
| 20 | 229th | SP Gavin Floyd ChA |
| 21 | 252nd | OF Denard Span Min |
| 22 | 253rd | OF Raul Ibanez Phi |
| 23 | 276th | 3B Chris Johnson Hou |
| 24 | 277th | 1B Dan Johnson TB |
| 25 | 300th | SS Asdrubal Cabrera Cle |
| 26 | 301st | SP Johan Santana NYN |
| 27 | 324th | SP Chris Young NYN |
| 28 | 325th | SP Freddy Garcia NYA |
| 29 | 348th | C Miguel Olivo Sea |