| Round | Overall | Player |
|---|---|---|
| 1 | 1st | 3B Alex Rodriguez NYA |
| 2 | 24th | 1B Justin Morneau Min |
| 3 | 25th | 2B Brandon Phillips Cin |
| 4 | 48th | C Joe Mauer Min |
| 5 | 49th | OF Alexis Rios Tor |
| 6 | 72nd | RP Francisco Rodriguez LAA |
| 7 | 73rd | RP J.J. Putz Sea |
| 8 | 96th | RP Jose Valverde Hou |
| 9 | 97th | SP Daisuke Matsuzaka Bos |
| 10 | 120th | OF Hideki Matsui NYA |
| 11 | 121st | SP Yovani Gallardo Mil |
| 12 | 144th | OF Pat Burrell TB |
| 13 | 145th | SS Khalil Greene SD |
| 14 | 168th | 1B Joey Votto Cin |
| 15 | 169th | SP Joe Blanton Phi |
| 16 | 192nd | OF J.D. Drew Bos |
| 17 | 193rd | SP Ian Snell Pit |
| 18 | 216th | 3B Eric Chavez Oak |
| 19 | 217th | SP Greg Maddux SD |
| 20 | 240th | SP Homer Bailey Cin |
| 21 | 241st | SS Julio Lugo Bos |
| 22 | 264th | C Kurt Suzuki Oak |
| 23 | 265th | RP B.J. Ryan Tor |
| 24 | 288th | OF Travis Buck Oak |
| 25 | 289th | SP Kyle Kendrick Phi |
| 26 | 312th | 2B Jose Lopez Sea |
| 27 | 313th | 1B Lyle Overbay Tor |
| 28 | 336th | OF Carlos Gomez Min |
| 29 | 337th | SP Shaun Marcum Tor |