| Round | Overall | Player |
|---|---|---|
| 1 | 6th | 1B Jeff Bagwell Hou |
| 2 | 19th | OF Manny Ramirez Bos |
| 3 | 30th | 1B Mark McGwire StL |
| 4 | 43rd | 2B Jose Vidro Mon |
| 5 | 54th | 3B Jeff Cirillo Col |
| 6 | 67th | SP Andy Pettitte NYA |
| 7 | 78th | SP David Wells ChA |
| 8 | 91st | SP Kevin Millwood Atl |
| 9 | 102nd | RP Matt Mantei Ari |
| 10 | 115th | SP Kris Benson Pit |
| 11 | 126th | SS Omar Vizquel Cle |
| 12 | 139th | OF Jeromy Burnitz Mil |
| 13 | 150th | OF Greg Vaughn TB |
| 14 | 163rd | C Ben Molina Ana |
| 15 | 174th | SP Jamie Moyer Sea |
| 16 | 187th | C Jason Varitek Bos |
| 17 | 198th | SP Ben Sheets Mil |
| 18 | 211th | SS Carlos Guillen Sea |
| 19 | 222nd | SP Randy Wolf Phi |
| 20 | 235th | 2B Damion Easley Det |
| 21 | 246th | OF Terrence Long Oak |
| 22 | 259th | OF Ray Lankford StL |
| 23 | 270th | SP John Halama Sea |
| 24 | 283rd | 3B Vinny Castilla Hou |
| 25 | 294th | 1B Mo Vaughn Ana |
| 26 | 307th | SP A.J. Burnett Fla |
| 27 | 318th | OF Dante Bichette Bos |
| 28 | 331st | 1B Mark Grace Ari |
| 29 | 342nd | SP Ryan Glynn Tex |