| Round | Overall | Player |
|---|---|---|
| 1 | 1st | SS Hanley Ramirez Fla |
| 2 | 24th | 1B Justin Morneau Min |
| 3 | 25th | SP Johan Santana NYN |
| 4 | 48th | 1B Adam Dunn Was |
| 5 | 49th | SP Jake Peavy ChA |
| 6 | 72nd | 1B Chris Davis Tex |
| 7 | 73rd | OF Matt Kemp LAD |
| 8 | 96th | SP Carlos Zambrano ChN |
| 9 | 97th | 3B Ryan Zimmerman Was |
| 10 | 120th | SP Derek Lowe Atl |
| 11 | 121st | C Ryan Doumit Pit |
| 12 | 144th | SP Josh Johnson Fla |
| 13 | 145th | OF Chris Young Ari |
| 14 | 168th | SS Mike Aviles KC |
| 15 | 169th | RP Brian Wilson SF |
| 16 | 192nd | 1B James Loney LAD |
| 17 | 193rd | 3B Ian Stewart Col |
| 18 | 216th | C Matt Wieters Bal |
| 19 | 217th | RP Brandon Morrow Sea |
| 20 | 240th | SP John Maine NYN |
| 21 | 241st | SP Chris Volstad Fla |
| 22 | 264th | OF Denard Span Min |
| 23 | 265th | 2B Kazuo Matsui Hou |
| 24 | 288th | OF David Murphy Tex |
| 25 | 289th | SP Randy Wolf LAD |
| 26 | 312th | RP Chris Ray Tex |
| 27 | 313th | 1B Jeff Clement Pit |
| 28 | 336th | SP Tommy Hanson Atl |
| 29 | 337th | 1B Travis Ishikawa SF |