| Round | Overall | Player |
|---|---|---|
| 1 | 7th | C Mike Piazza NYN |
| 2 | 18th | SS Derek Jeter NYA |
| 3 | 31st | SP Mike Mussina NYA |
| 4 | 42nd | 1B Phil Nevin SD |
| 5 | 55th | 1B Jim Thome Cle |
| 6 | 66th | OF Andruw Jones Atl |
| 7 | 79th | SP Wade Miller Hou |
| 8 | 90th | SP Tom Glavine Atl |
| 9 | 103rd | SP Bartolo Colon Cle |
| 10 | 114th | SP Eric Milton Min |
| 11 | 127th | OF Preston Wilson Fla |
| 12 | 138th | 3B Sean Burroughs SD |
| 13 | 151st | SP Woody Williams StL |
| 14 | 162nd | SP Aaron Sele Ana |
| 15 | 175th | SP Kevin Millwood Atl |
| 16 | 186th | SS Edgar Renteria StL |
| 17 | 199th | OF Bob Higginson Det |
| 18 | 210th | 3B Eric Hinske Tor |
| 19 | 223rd | 2B Marcus Giles Atl |
| 20 | 234th | SP Brian Lawrence SD |
| 21 | 247th | 1B Jay Gibbons Bal |
| 22 | 258th | OF Torii Hunter Min |
| 23 | 271st | 2B D'Angelo Jimenez SD |
| 24 | 282nd | SP Terry Adams Phi |
| 25 | 295th | SP Scott Schoeneweis Ana |
| 26 | 306th | C Raul Casanova Mil |
| 27 | 319th | OF Bubba Trammell SD |
| 28 | 330th | SP Ryan Drese Cle |
| 29 | 343rd | SP Jorge Julio Bal |