| Round | Overall | Player |
|---|---|---|
| 1 | 1st | 3B Alex Rodriguez NYA |
| 2 | 24th | 1B Justin Morneau Min |
| 3 | 25th | OF Adam Dunn Ari |
| 4 | 48th | C Joe Mauer Min |
| 5 | 49th | OF Hideki Matsui NYA |
| 6 | 72nd | OF Andruw Jones LAD |
| 7 | 73rd | 3B Ryan Zimmerman Was |
| 8 | 96th | SP Chris Young SD |
| 9 | 97th | SP Chien-Ming Wang NYA |
| 10 | 120th | SS Khalil Greene SD |
| 11 | 121st | OF Kosuke Fukudome ChN |
| 12 | 144th | SP John Lackey LAA |
| 13 | 145th | SP Jeff Francis Col |
| 14 | 168th | RP Joe Borowski Cle |
| 15 | 169th | RP Kerry Wood ChN |
| 16 | 192nd | 2B Aaron Hill Tor |
| 17 | 193rd | C Jason Varitek Bos |
| 18 | 216th | RP Brandon Lyon Det |
| 19 | 217th | SP Johnny Cueto Cin |
| 20 | 240th | 1B Adam LaRoche Pit |
| 21 | 241st | SP Greg Maddux SD |
| 22 | 264th | SP Mark Prior SD |
| 23 | 265th | SP Clayton Kershaw LAD |
| 24 | 288th | SS Alexei Ramirez ChA |
| 25 | 289th | OF Jay Bruce Cin |
| 26 | 312th | SP Randy Wolf LAD |
| 27 | 313th | 3B Joe Crede ChA |
| 28 | 336th | SS Ryan Theriot ChN |
| 29 | 337th | SP John Danks ChA |