| Round | Overall | Player |
|---|---|---|
| 1 | 12th | OF Andruw Jones Atl |
| 2 | 13th | SP Johan Santana Min |
| 3 | 36th | 1B Paul Konerko ChA |
| 4 | 37th | SP Roy Oswalt Hou |
| 5 | 60th | 3B Ryan Zimmerman Was |
| 6 | 61st | SP Justin Verlander Det |
| 7 | 84th | 2B Robinson Cano NYA |
| 8 | 85th | SP Aaron Harang Cin |
| 9 | 108th | OF Alexis Rios Tor |
| 10 | 109th | RP Bobby Jenks ChA |
| 11 | 132nd | C Kenji Johjima Sea |
| 12 | 133rd | SP Jon Garland LAA |
| 13 | 156th | OF Josh Willingham Fla |
| 14 | 157th | RP Jose Valverde Hou |
| 15 | 180th | OF Austin Kearns Was |
| 16 | 181st | RP Joe Borowski Cle |
| 17 | 204th | SS Jhonny Peralta Cle |
| 18 | 205th | OF Jacque Jones Det |
| 19 | 228th | SP Chad Billingsley LAD |
| 20 | 229th | 3B Melvin Mora Bal |
| 21 | 252nd | OF Juan Pierre LAD |
| 22 | 253rd | OF Willy Taveras Col |
| 23 | 276th | 2B Luis Castillo NYN |
| 24 | 277th | SS Yuniesky Betancourt Sea |
| 25 | 300th | SP Tom Gorzelanny Pit |
| 26 | 301st | C Paul Lo Duca Was |
| 27 | 324th | RP Dave Weathers Cin |
| 28 | 325th | SP Joel Zumaya Det |
| 29 | 348th | 1B Kevin Millar Bal |