| Round | Overall | Player |
|---|---|---|
| 1 | 7th | OF Barry Bonds SF |
| 2 | 18th | OF Carlos Beltran Hou |
| 3 | 31st | RP Billy Wagner Phi |
| 4 | 42nd | RP Keith Foulke Bos |
| 5 | 55th | C Javy Lopez Bal |
| 6 | 66th | OF Aubrey Huff TB |
| 7 | 79th | 1B Mike Sweeney KC |
| 8 | 90th | 3B Morgan Ensberg Hou |
| 9 | 103rd | RP Trevor Hoffman SD |
| 10 | 114th | SP Jose Contreras ChA |
| 11 | 127th | SS Alex Cintron Ari |
| 12 | 138th | 2B Placido Polanco Phi |
| 13 | 151st | OF Larry Walker StL |
| 14 | 162nd | RP Dan Kolb Mil |
| 15 | 175th | SP C.C. Sabathia Cle |
| 16 | 186th | SP Brad Penny LA |
| 17 | 199th | 1B Brad Fullmer Tex |
| 18 | 210th | SP Jake Peavy SD |
| 19 | 223rd | 1B Jay Gibbons Bal |
| 20 | 234th | 3B Vinny Castilla Col |
| 21 | 247th | 2B Mark Loretta SD |
| 22 | 258th | SP Brian Anderson KC |
| 23 | 271st | 2B Brian Roberts Bal |
| 24 | 282nd | RP Danys Baez TB |
| 25 | 295th | SP Ted Lilly Tor |
| 26 | 306th | 1B Jeff Conine Fla |
| 27 | 319th | OF Jose Cruz Jr TB |
| 28 | 330th | C Damian Miller Oak |
| 29 | 343rd | RP Tim Worrell Phi |