| Round | Overall | Player |
|---|---|---|
| 1 | 5th | 1B Jason Giambi NYA |
| 2 | 20th | 3B Albert Pujols StL |
| 3 | 29th | SP Mike Mussina NYA |
| 4 | 44th | OF Bernie Williams NYA |
| 5 | 53rd | RP Kazuhiro Sasaki Sea |
| 6 | 68th | SS Jimmy Rollins Phi |
| 7 | 77th | OF Ryan Klesko SD |
| 8 | 92nd | SP Bartolo Colon Cle |
| 9 | 101st | RP Danny Graves Cin |
| 10 | 116th | C Mike Lieberthal Phi |
| 11 | 125th | OF Raul Mondesi Tor |
| 12 | 140th | SP C.C. Sabathia Cle |
| 13 | 149th | SP Ryan Dempster Fla |
| 14 | 164th | 2B Luis Castillo Fla |
| 15 | 173rd | OF Matt Lawton Cle |
| 16 | 188th | SP Todd Ritchie ChA |
| 17 | 197th | OF Torii Hunter Min |
| 18 | 212th | 3B Morgan Ensberg Hou |
| 19 | 221st | OF Terrence Long Oak |
| 20 | 236th | SP Dustin Hermanson Bos |
| 21 | 245th | SP Mark Prior ChN |
| 22 | 260th | DH David Ortiz Min |
| 23 | 269th | SP Albie Lopez Atl |
| 24 | 284th | 1B Kevin Young Pit |
| 25 | 293rd | 2B Jerry Hairston Jr. Bal |
| 26 | 308th | OF Austin Kearns Cin |
| 27 | 317th | SS Adam Everett Hou |
| 28 | 332nd | C Einar Diaz Cle |
| 29 | 341st | SP Dave Burba Tex |