| Round | Overall | Player |
|---|---|---|
| 1 | 12th | 1B Jim Thome Phi |
| 2 | 13th | C Mike Piazza NYN |
| 3 | 36th | SP Roy Halladay Tor |
| 4 | 37th | 3B Troy Glaus Ana |
| 5 | 60th | OF Bernie Williams NYA |
| 6 | 61st | SP Tom Glavine NYN |
| 7 | 84th | SP Kevin Millwood Phi |
| 8 | 85th | OF Torii Hunter Min |
| 9 | 108th | OF Jacque Jones Min |
| 10 | 109th | 2B Junior Spivey Ari |
| 11 | 132nd | SP A.J. Burnett Fla |
| 12 | 133rd | SS David Eckstein Ana |
| 13 | 156th | SP Paul Byrd Atl |
| 14 | 157th | SP David Wells NYA |
| 15 | 180th | 3B David Bell Phi |
| 16 | 181st | RP Jason Isringhausen StL |
| 17 | 204th | SP Rick Reed Min |
| 18 | 205th | C Michael Barrett Mon |
| 19 | 228th | 3B Mark Bellhorn Col |
| 20 | 229th | 2B Placido Polanco Phi |
| 21 | 252nd | 1B Scott Hatteberg Oak |
| 22 | 253rd | SS Juan Uribe Col |
| 23 | 276th | OF J.D. Drew StL |
| 24 | 277th | OF Brad Wilkerson Mon |
| 25 | 300th | OF Terrence Long Oak |
| 26 | 301st | SP Brandon Duckworth Phi |
| 27 | 324th | SP Brett Tomko StL |
| 28 | 325th | RP Bob Wickman Cle |
| 29 | 348th | 1B Doug Mientkiewicz Min |