| Round | Overall | Player |
|---|---|---|
| 1 | 6th | 1B Jim Thome Phi |
| 2 | 19th | OF Gary Sheffield NYA |
| 3 | 30th | OF Lance Berkman Hou |
| 4 | 43rd | RP Mariano Rivera NYA |
| 5 | 54th | RP Octavio Dotel Oak |
| 6 | 67th | SP Randy Wolf Phi |
| 7 | 78th | OF Ryan Klesko SD |
| 8 | 91st | SP Jamie Moyer Sea |
| 9 | 102nd | SS Jose Reyes NYN |
| 10 | 115th | SP Freddy Garcia ChA |
| 11 | 126th | SP C.C. Sabathia Cle |
| 12 | 139th | OF Richard Hidalgo NYN |
| 13 | 150th | SP Livan Hernandez Mon |
| 14 | 163rd | SS Alex Cintron Ari |
| 15 | 174th | 2B Junior Spivey Mil |
| 16 | 187th | C Ramon Castro Fla |
| 17 | 198th | 3B Melvin Mora Bal |
| 18 | 211th | SP Carl Pavano Fla |
| 19 | 222nd | OF Mike Cameron NYN |
| 20 | 235th | 1B Brad Fullmer Tex |
| 21 | 246th | SP John Lackey Ana |
| 22 | 259th | SP Kris Benson NYN |
| 23 | 270th | C Victor Martinez Cle |
| 24 | 283rd | 3B Wes Helms Mil |
| 25 | 294th | 1B Ben Broussard Cle |
| 26 | 307th | SP Steve Trachsel NYN |
| 27 | 318th | 2B Brian Roberts Bal |
| 28 | 331st | SP Jae Weong Seo NYN |
| 29 | 342nd | 1B Carlos Pena Det |