| Round | Overall | Player |
|---|---|---|
| 1 | 1st | 3B Alex Rodriguez NYA |
| 2 | 24th | SP Roy Oswalt Hou |
| 3 | 25th | 1B Carlos Delgado NYN |
| 4 | 48th | SS Jimmy Rollins Phi |
| 5 | 49th | SP Dontrelle Willis Fla |
| 6 | 72nd | RP Chad Cordero Was |
| 7 | 73rd | SP Andy Pettitte Hou |
| 8 | 96th | SP Barry Zito Oak |
| 9 | 97th | 1B Justin Morneau Min |
| 10 | 120th | 2B Tadahito Iguchi ChA |
| 11 | 121st | OF Jeremy Hermida Fla |
| 12 | 144th | RP Armando Benitez SF |
| 13 | 145th | SP Jeremy Bonderman Det |
| 14 | 168th | C Ramon Hernandez Bal |
| 15 | 169th | OF Nick Swisher Oak |
| 16 | 192nd | OF Wily Pena Bos |
| 17 | 193rd | SP Odalis Perez KC |
| 18 | 216th | OF David Dellucci Cle |
| 19 | 217th | 3B Garrett Atkins Col |
| 20 | 240th | OF Bill Hall Mil |
| 21 | 241st | C Ben Molina SF |
| 22 | 264th | OF Ryan Freel Cin |
| 23 | 265th | SP Paul Maholm Pit |
| 24 | 288th | 1B Adam LaRoche Pit |
| 25 | 289th | OF Brian N. Anderson ChA |
| 26 | 312th | SP Aaron Cook Col |
| 27 | 313th | SP Horacio Ramirez Atl |
| 28 | 336th | RP Danys Baez Bal |