| Round | Overall | Player |
|---|---|---|
| 1 | 3rd | OF Alfonso Soriano Tex |
| 2 | 22nd | C Victor Martinez Cle |
| 3 | 27th | SP Pedro Martinez NYN |
| 4 | 46th | DH Travis Hafner Cle |
| 5 | 51st | SS Jimmy Rollins Phi |
| 6 | 70th | OF Andruw Jones Atl |
| 7 | 75th | 1B Justin Morneau Min |
| 8 | 94th | SP Mark Buehrle ChA |
| 9 | 99th | 3B David Wright NYN |
| 10 | 118th | RP Braden Looper NYN |
| 11 | 123rd | OF Austin Kearns Cin |
| 12 | 142nd | SP Brandon Webb Ari |
| 13 | 147th | OF Preston Wilson Was |
| 14 | 166th | SP Jon Lieber Phi |
| 15 | 171st | SP Kelvim Escobar LAA |
| 16 | 190th | RP B.J. Ryan Bal |
| 17 | 195th | SP Bronson Arroyo Bos |
| 18 | 214th | 1B Rafael Palmeiro Bal |
| 19 | 219th | 3B Dallas McPherson LAA |
| 20 | 238th | 3B D'Angelo Jimenez Cin |
| 21 | 243rd | OF Matt Holliday Col |
| 22 | 262nd | OF Milton Bradley LAD |
| 23 | 267th | C J.D. Closser Col |
| 24 | 286th | SP Erik Bedard Bal |
| 25 | 291st | SP Miguel Batista Tor |
| 26 | 310th | SP Jose Contreras ChA |
| 27 | 315th | SS Jhonny Peralta Cle |
| 28 | 334th | SP Wilfredo Ledezma Det |
| 29 | 339th | 2B Jorge Cantu TB |