| Round | Overall | Player |
|---|---|---|
| 1 | 10th | OF Albert Pujols StL |
| 2 | 15th | RP Eric Gagne LA |
| 3 | 34th | 1B Rafael Palmeiro Tex |
| 4 | 39th | SP Bartolo Colon ChA |
| 5 | 58th | OF Carlos Beltran KC |
| 6 | 63rd | RP Billy Koch ChA |
| 7 | 82nd | OF Johnny Damon Bos |
| 8 | 87th | SP Jamie Moyer Sea |
| 9 | 106th | 2B Junior Spivey Ari |
| 10 | 111th | SP Russ Ortiz Atl |
| 11 | 130th | SS David Eckstein Ana |
| 12 | 135th | 3B Tony Batista Bal |
| 13 | 154th | 1B John Olerud Sea |
| 14 | 159th | OF Randy Winn Sea |
| 15 | 178th | SP Jake Peavy SD |
| 16 | 183rd | SP Paul Byrd Atl |
| 17 | 202nd | SP Kirk Rueter SF |
| 18 | 207th | SP Kip Wells Pit |
| 19 | 226th | C Brad Ausmus Hou |
| 20 | 231st | OF Steve Finley Ari |
| 21 | 250th | SP Steve Trachsel NYN |
| 22 | 255th | SS Jose Nieves NYA |
| 23 | 274th | 2B Adam Kennedy Ana |
| 24 | 279th | 3B Joe Randa KC |
| 25 | 298th | SP Jimmy Haynes Cin |
| 26 | 303rd | OF Juan Pierre Fla |
| 27 | 322nd | C Geronimo Gil Bal |
| 28 | 327th | SS Ramon Vazquez SD |
| 29 | 346th | SP Glendon Rusch Mil |