| Round | Overall | Player |
|---|---|---|
| 1 | 8th | OF Barry Bonds SF |
| 2 | 17th | SP Roy Halladay Tor |
| 3 | 32nd | 2B Jeff Kent Hou |
| 4 | 41st | SP Randy Johnson Ari |
| 5 | 56th | OF Andruw Jones Atl |
| 6 | 65th | RP Troy Percival Ana |
| 7 | 80th | 1B Rafael Palmeiro Bal |
| 8 | 89th | SP Carlos Zambrano ChN |
| 9 | 104th | 1B David Ortiz Bos |
| 10 | 113th | OF Juan Gonzalez KC |
| 11 | 128th | SP C.C. Sabathia Cle |
| 12 | 137th | 3B Joe Crede ChA |
| 13 | 152nd | 2B Placido Polanco Phi |
| 14 | 161st | SP Mike Hampton Atl |
| 15 | 176th | SP Carl Pavano Fla |
| 16 | 185th | SS Rich Aurilia SD |
| 17 | 200th | 3B Melvin Mora Bal |
| 18 | 209th | OF Milton Bradley LA |
| 19 | 224th | SP Adam Eaton SD |
| 20 | 233rd | SP Shawn Chacon Col |
| 21 | 248th | OF Moises Alou ChN |
| 22 | 257th | 1B John Olerud NYA |
| 23 | 272nd | OF Marlon Byrd Phi |
| 24 | 281st | SP Jon Garland ChA |
| 25 | 296th | SS Carlos Guillen Det |
| 26 | 305th | RP Billy Koch Fla |
| 27 | 320th | C Jason LaRue Cin |
| 28 | 329th | C Robby Hammock Ari |
| 29 | 344th | SP Jose Acevedo Cin |