| Round | Overall | Player |
|---|---|---|
| 1 | 12th | 3B David Wright NYN |
| 2 | 13th | OF Bobby Abreu NYA |
| 3 | 36th | SP Chris Carpenter StL |
| 4 | 37th | RP Mariano Rivera NYA |
| 5 | 60th | SP Rich Harden Oak |
| 6 | 61st | 1B Jason Giambi NYA |
| 7 | 84th | OF Jeff Francoeur Atl |
| 8 | 85th | OF Brian S. Giles SD |
| 9 | 108th | SP A.J. Burnett Tor |
| 10 | 109th | SS Rafael Furcal LAD |
| 11 | 132nd | OF Jeremy Hermida Fla |
| 12 | 133rd | 2B Robinson Cano NYA |
| 13 | 156th | SP Jake Westbrook Cle |
| 14 | 157th | RP Jose Valverde Ari |
| 15 | 180th | 1B Dan Johnson Oak |
| 16 | 181st | SP Tom Glavine NYN |
| 17 | 204th | 3B Ryan Zimmerman Was |
| 18 | 205th | SP Aaron Harang Cin |
| 19 | 228th | SP Jarrod Washburn Sea |
| 20 | 229th | OF Garret Anderson LAA |
| 21 | 252nd | SP Gustavo Chacin Tor |
| 22 | 253rd | SS J.J. Hardy Mil |
| 23 | 276th | 2B Jose Castillo Pit |
| 24 | 277th | OF Jose Cruz Jr LAD |
| 25 | 300th | C Jason Kendall Oak |
| 26 | 301st | SP David Wells SD |
| 27 | 324th | 1B Shea Hillenbrand LAA |
| 28 | 325th | SP Brandon Backe Hou |
| 29 | 348th | SP Ted Lilly ChA |