| Round | Overall | Player |
|---|---|---|
| 1 | 12th | SP Johan Santana NYN |
| 2 | 13th | OF Grady Sizemore Cle |
| 3 | 36th | SS Troy Tulowitzki Col |
| 4 | 37th | SP C.C. Sabathia Mil |
| 5 | 60th | C Joe Mauer Min |
| 6 | 61st | RP Bobby Jenks ChA |
| 7 | 84th | 3B Chone Figgins LAA |
| 8 | 85th | OF Hunter Pence Hou |
| 9 | 108th | 1B Adam LaRoche Pit |
| 10 | 109th | SP John Maine NYN |
| 11 | 132nd | SP Chad Billingsley LAD |
| 12 | 133rd | OF Pat Burrell TB |
| 13 | 156th | SP Matt Capps Pit |
| 14 | 157th | 2B Jeff Kent LAD |
| 15 | 180th | SP Ian Snell Pit |
| 16 | 181st | DH Hank Blalock Tex |
| 17 | 204th | OF J.D. Drew Bos |
| 18 | 205th | RP Eric Gagne Mil |
| 19 | 228th | 1B Daric Barton Oak |
| 20 | 229th | 2B Akinori Iwamura TB |
| 21 | 252nd | SP Jair Jurrjens Atl |
| 22 | 253rd | C John Buck KC |
| 23 | 276th | SP Hiroki Kuroda LAD |
| 24 | 277th | OF Geoff Jenkins Phi |
| 25 | 300th | SS Jack Wilson Pit |
| 26 | 301st | SP Johnny Cueto Cin |
| 27 | 324th | SP Daniel Cabrera Bal |
| 28 | 325th | 1B Nomar Garciaparra LAD |
| 29 | 348th | OF Matt Diaz Atl |