| Round | Overall | Player |
|---|---|---|
| 1 | 8th | 1B Todd Helton Col |
| 2 | 17th | OF Andruw Jones Atl |
| 3 | 32nd | SP Tim Hudson Oak |
| 4 | 41st | 3B Fernando Tatis Mon |
| 5 | 56th | RP Billy Koch Tor |
| 6 | 65th | OF Shannon Stewart Tor |
| 7 | 80th | SP Kevin Millwood Atl |
| 8 | 89th | SP Kerry Wood ChN |
| 9 | 104th | 1B Paul Konerko ChA |
| 10 | 113th | RP Danny Graves Cin |
| 11 | 128th | 2B Jose Ortiz Oak |
| 12 | 137th | SS Neifi Perez Col |
| 13 | 152nd | OF Carlos Lee ChA |
| 14 | 161st | SP Matt Morris StL |
| 15 | 176th | C Jason Varitek Bos |
| 16 | 185th | SP Robert Person Phi |
| 17 | 200th | OF Rondell White ChN |
| 18 | 209th | OF Brian Jordan Atl |
| 19 | 224th | RP Tom Gordon ChN |
| 20 | 233rd | C Ramon Hernandez Oak |
| 21 | 248th | SP Jose Lima Hou |
| 22 | 257th | 2B Quilvio Veras Atl |
| 23 | 272nd | SP Pete Harnisch Cin |
| 24 | 281st | SP Pedro Astacio Col |
| 25 | 296th | 3B Aramis Ramirez Pit |
| 26 | 305th | OF Jose Cruz Jr Tor |
| 27 | 320th | SS Melvin Mora Bal |
| 28 | 329th | 1B David Ortiz Min |
| 29 | 344th | SP Doug Davis Tex |