| Round | Overall | Player |
|---|---|---|
| 1 | 1st | 3B Alex Rodriguez NYA |
| 2 | 24th | SP Roy Oswalt Hou |
| 3 | 25th | OF Andruw Jones Atl |
| 4 | 48th | SP Randy Johnson NYA |
| 5 | 49th | OF Pat Burrell Phi |
| 6 | 72nd | SP Andy Pettitte Hou |
| 7 | 73rd | 1B Justin Morneau Min |
| 8 | 96th | SP Cliff Lee Cle |
| 9 | 97th | C Ivan Rodriguez Det |
| 10 | 120th | RP B.J. Ryan Tor |
| 11 | 121st | 3B Melvin Mora Bal |
| 12 | 144th | SP Jose Contreras ChA |
| 13 | 145th | OF Moises Alou SF |
| 14 | 168th | RP Ryan Dempster ChN |
| 15 | 169th | 2B Mark Loretta Bos |
| 16 | 192nd | SS Julio Lugo Bos |
| 17 | 193rd | RP Jose Valverde Ari |
| 18 | 216th | OF Scott Podsednik ChA |
| 19 | 217th | OF Rocco Baldelli TB |
| 20 | 240th | C Paul Lo Duca NYN |
| 21 | 241st | 3B Mike Lowell Bos |
| 22 | 264th | SP Aaron Harang Cin |
| 23 | 265th | 1B Adam LaRoche Pit |
| 24 | 288th | SS J.J. Hardy Mil |
| 25 | 289th | OF Brady Clark Mil |
| 26 | 312th | 2B Todd Walker SD |
| 27 | 313th | RP Brian Fuentes Col |
| 28 | 336th | SP Brandon Claussen Cin |
| 29 | 337th | SP Brandon McCarthy Tex |