| Round | Overall | Player |
|---|---|---|
| 1 | 3rd | OF Matt Holliday Col |
| 2 | 22nd | SP Jake Peavy SD |
| 3 | 27th | 1B Justin Morneau Min |
| 4 | 46th | OF Carl Crawford TB |
| 5 | 51st | SP Roy Halladay Tor |
| 6 | 70th | 2B Robinson Cano NYA |
| 7 | 75th | RP Billy Wagner NYN |
| 8 | 94th | 3B Mike Young Tex |
| 9 | 99th | RP Francisco Cordero Cin |
| 10 | 118th | SP Brad Penny LAD |
| 11 | 123rd | 3B Alex Gordon KC |
| 12 | 142nd | SP Jeff Francis Col |
| 13 | 147th | C Kenji Johjima Sea |
| 14 | 166th | OF Rick Ankiel StL |
| 15 | 171st | SP Ted Lilly ChN |
| 16 | 190th | 1B Richie Sexson Sea |
| 17 | 195th | OF J.D. Drew Bos |
| 18 | 214th | SP Jon Lester Bos |
| 19 | 219th | SS Stephen Drew Ari |
| 20 | 238th | SP Nate Robertson Det |
| 21 | 243rd | 3B Eric Chavez Oak |
| 22 | 262nd | OF Lastings Milledge Was |
| 23 | 267th | SP Mike Mussina NYA |
| 24 | 286th | 2B Luis Castillo NYN |
| 25 | 291st | SP Jason Schmidt LAD |
| 26 | 310th | RP Tom Gordon Ari |
| 27 | 315th | C Ryan Doumit Pit |
| 28 | 334th | 3B Joe Crede ChA |
| 29 | 339th | SP Chuck James Atl |