| Round | Overall | Player |
|---|---|---|
| 1 | 10th | 3B David Wright NYN |
| 2 | 15th | DH Travis Hafner Cle |
| 3 | 34th | OF Jermaine Dye ChA |
| 4 | 39th | 1B Carlos Delgado NYN |
| 5 | 58th | RP Bobby Jenks ChA |
| 6 | 63rd | SP John Smoltz Atl |
| 7 | 82nd | 2B Robinson Cano NYA |
| 8 | 87th | OF Michael Cuddyer Min |
| 9 | 106th | SP Erik Bedard Bal |
| 10 | 111th | RP J.J. Putz Sea |
| 11 | 130th | C Russell Martin LAD |
| 12 | 135th | OF Nick Markakis Bal |
| 13 | 154th | SP Jon Garland LAA |
| 14 | 159th | SS Orlando Cabrera ChA |
| 15 | 178th | OF Craig Monroe Min |
| 16 | 183rd | SP Kevin Millwood Tex |
| 17 | 202nd | SP Joe Blanton Oak |
| 18 | 207th | 3B Joe Crede ChA |
| 19 | 226th | 1B Conor Jackson Ari |
| 20 | 231st | OF Curtis Granderson Det |
| 21 | 250th | RP Josh Johnson Fla |
| 22 | 255th | RP Kerry Wood ChN |
| 23 | 274th | 2B Craig Biggio Hou |
| 24 | 279th | SP Woody Williams Hou |
| 25 | 298th | C Jason Kendall Mil |
| 26 | 303rd | OF David Roberts SF |
| 27 | 322nd | SP Mark Prior ChN |
| 28 | 327th | SP Jarrod Washburn Sea |
| 29 | 346th | SP Shawn Hill Was |