| Round | Overall | Player |
|---|---|---|
| 1 | 9th | SS Mike Young Tex |
| 2 | 16th | OF Bobby Abreu NYA |
| 3 | 33rd | SP Jake Peavy SD |
| 4 | 40th | SP Roy Halladay Tor |
| 5 | 57th | 3B Eric Chavez Oak |
| 6 | 64th | OF Vernon Wells Tor |
| 7 | 81st | C Joe Mauer Min |
| 8 | 88th | 2B Robinson Cano NYA |
| 9 | 105th | SP Andy Pettitte Hou |
| 10 | 112th | OF Jonny Gomes TB |
| 11 | 129th | 1B Prince Fielder Mil |
| 12 | 136th | SP Jeremy Bonderman Det |
| 13 | 153rd | SP Matt Cain SF |
| 14 | 160th | SP Scott Kazmir TB |
| 15 | 177th | OF Preston Wilson StL |
| 16 | 184th | SP Doug Davis Ari |
| 17 | 201st | SP Kelvim Escobar LAA |
| 18 | 208th | SP Chien-Ming Wang NYA |
| 19 | 225th | SP Justin Verlander Det |
| 20 | 232nd | 1B Casey Kotchman LAA |
| 21 | 249th | 1B Conor Jackson Ari |
| 22 | 256th | OF Scott Podsednik ChA |
| 23 | 273rd | OF Delmon Young TB |
| 24 | 280th | SP Aaron Heilman NYN |
| 25 | 297th | 2B Jose Castillo Pit |
| 26 | 304th | SS Omar Vizquel SF |
| 27 | 321st | 3B Joe Randa Pit |
| 28 | 328th | SS Stephen Drew Ari |
| 29 | 345th | C Javier Valentin Cin |