| Round | Overall | Player |
|---|---|---|
| 1 | 3rd | SP Randy Johnson Ari |
| 2 | 22nd | OF Carlos Beltran KC |
| 3 | 27th | OF Chipper Jones Atl |
| 4 | 46th | 1B Paul Konerko ChA |
| 5 | 51st | 2B Jose Vidro Mon |
| 6 | 70th | RP Billy Koch ChA |
| 7 | 75th | SP Odalis Perez LA |
| 8 | 94th | 3B Mike Lowell Fla |
| 9 | 99th | C Charles Johnson Col |
| 10 | 118th | SS Jose Valentin ChA |
| 11 | 123rd | SP Vicente Padilla Phi |
| 12 | 142nd | RP Scott Williamson Bos |
| 13 | 147th | OF Austin Kearns Cin |
| 14 | 166th | SP Damian Moss Bal |
| 15 | 171st | OF Vernon Wells Tor |
| 16 | 190th | 3B Adrian Beltre LA |
| 17 | 195th | DH Ellis Burks Cle |
| 18 | 214th | OF Karim Garcia NYA |
| 19 | 219th | SP Brett Myers Phi |
| 20 | 238th | 1B Scott Hatteberg Oak |
| 21 | 243rd | 2B Brandon Phillips Cle |
| 22 | 262nd | SP Steve Trachsel NYN |
| 23 | 267th | OF Mark Kotsay SD |
| 24 | 286th | SP Carlos Zambrano ChN |
| 25 | 291st | SP Adam Eaton SD |
| 26 | 310th | C Miguel Olivo ChA |
| 27 | 315th | SS Ramon Vazquez SD |
| 28 | 334th | 3B Brandon Larson Cin |
| 29 | 339th | RP Scott Stewart Mon |