| Round | Overall | Player |
|---|---|---|
| 1 | 12th | OF Carlos Beltran Hou |
| 2 | 13th | SP Curt Schilling Bos |
| 3 | 36th | SP Randy Johnson Ari |
| 4 | 37th | SP John Smoltz Atl |
| 5 | 60th | 3B Chipper Jones Atl |
| 6 | 61st | 1B Derrek Lee ChN |
| 7 | 84th | SP Jason Schmidt SF |
| 8 | 85th | 2B Kazuo Matsui NYN |
| 9 | 108th | RP Jason Isringhausen StL |
| 10 | 109th | SP Derek Lowe Bos |
| 11 | 132nd | 3B Corey Koskie Min |
| 12 | 133rd | C Jason Kendall Pit |
| 13 | 156th | 2B Ray Durham SF |
| 14 | 157th | OF Juan Pierre Fla |
| 15 | 180th | 1B Kevin Millar Bos |
| 16 | 181st | RP Robb Nen SF |
| 17 | 204th | 1B Paul Konerko ChA |
| 18 | 205th | OF Dmitri Young Det |
| 19 | 228th | 3B Joe Crede ChA |
| 20 | 229th | SP Ben Sheets Mil |
| 21 | 252nd | SP Brian Anderson KC |
| 22 | 253rd | OF Juan Encarnacion Fla |
| 23 | 276th | SS Cristian Guzman Min |
| 24 | 277th | 3B D'Angelo Jimenez Cin |
| 25 | 300th | RP Danny Graves Cin |
| 26 | 301st | 1B Jason Phillips NYN |
| 27 | 324th | SP Oliver Perez Pit |
| 28 | 325th | C Robby Hammock Ari |
| 29 | 348th | 2B Neifi Perez SF |