| Round | Overall | Player |
|---|---|---|
| 1 | 4th | 1B Todd Helton Col |
| 2 | 21st | SP Mark Prior ChN |
| 3 | 28th | OF Lance Berkman Hou |
| 4 | 45th | SP John Smoltz Atl |
| 5 | 52nd | 3B Chipper Jones Atl |
| 6 | 69th | 3B Mike Lowell Fla |
| 7 | 76th | RP Troy Percival Ana |
| 8 | 93rd | SP Dontrelle Willis Fla |
| 9 | 100th | OF Trot Nixon Bos |
| 10 | 117th | SP Esteban Loaiza NYA |
| 11 | 124th | OF Cliff Floyd NYN |
| 12 | 141st | C Jason Kendall Pit |
| 13 | 148th | SP C.C. Sabathia Cle |
| 14 | 165th | 2B Luis Castillo Fla |
| 15 | 172nd | RP Dan Kolb Mil |
| 16 | 189th | 1B Erubiel Durazo Oak |
| 17 | 196th | SP Horacio Ramirez Atl |
| 18 | 213th | SS Julio Lugo TB |
| 19 | 220th | OF Marlon Byrd Phi |
| 20 | 237th | SP Tony Armas Jr. Mon |
| 21 | 244th | RP Damaso Marte ChA |
| 22 | 261st | SP Jae Weong Seo NYN |
| 23 | 268th | SP Adam Eaton SD |
| 24 | 285th | SP Kazuhisa Ishii LA |
| 25 | 292nd | 3B Wes Helms Mil |
| 26 | 309th | C Jason LaRue Cin |
| 27 | 316th | 2B Luis Rivas Min |
| 28 | 333rd | 3B Alex Gonzalez TB |
| 29 | 340th | SP Elmer Dessens Ari |