| Round | Overall | Player |
|---|---|---|
| 1 | 6th | OF Barry Bonds SF |
| 2 | 19th | OF Larry Walker Col |
| 3 | 30th | OF Chipper Jones Atl |
| 4 | 43rd | 1B Richie Sexson Mil |
| 5 | 54th | 3B Scott Rolen Phi |
| 6 | 67th | SP Barry Zito Oak |
| 7 | 78th | SP Kerry Wood ChN |
| 8 | 91st | SP Chan Ho Park Tex |
| 9 | 102nd | 2B Craig Biggio Hou |
| 10 | 115th | C Mike Lieberthal Phi |
| 11 | 126th | OF Johnny Damon Bos |
| 12 | 139th | SP Jeff Weaver Det |
| 13 | 150th | SP Roy Halladay Tor |
| 14 | 163rd | SS Barry Larkin Cin |
| 15 | 174th | 3B Aaron Boone Cin |
| 16 | 187th | OF Todd Hollandsworth Col |
| 17 | 198th | SP Eric Gagne LA |
| 18 | 211th | SS Felipe Lopez Tor |
| 19 | 222nd | DH Nick Johnson NYA |
| 20 | 235th | SP Carlos Hernandez Hou |
| 21 | 246th | 2B Ron Belliard Mil |
| 22 | 259th | SP Paul Wilson TB |
| 23 | 270th | C Mitch Meluskey Det |
| 24 | 283rd | SS Omar Vizquel Cle |
| 25 | 294th | SP Odalis Perez LA |
| 26 | 307th | SP Jamey Wright Mil |
| 27 | 318th | 1B Steve Cox TB |
| 28 | 331st | OF Jeff Conine Bal |
| 29 | 342nd | RP Willis Roberts Bal |