| Round | Overall | Player |
|---|---|---|
| 1 | 12th | OF Josh Hamilton Tex |
| 2 | 13th | 1B Mark Teixeira NYA |
| 3 | 36th | OF Carlos Quentin ChA |
| 4 | 37th | 1B Adrian Gonzalez SD |
| 5 | 60th | SP John Lackey Bos |
| 6 | 61st | C Victor Martinez Bos |
| 7 | 84th | 3B Jhonny Peralta Cle |
| 8 | 85th | SP Ryan Dempster ChN |
| 9 | 108th | SP Yovani Gallardo Mil |
| 10 | 109th | OF Corey Hart Mil |
| 11 | 132nd | SP Josh Johnson Fla |
| 12 | 133rd | SP Kevin Slowey Min |
| 13 | 156th | SP Chris Carpenter StL |
| 14 | 157th | 3B Melvin Mora Bal |
| 15 | 180th | SP Roberto Hernandez Cle |
| 16 | 181st | RP Chad Qualls Ari |
| 17 | 204th | RP Frank Francisco Tex |
| 18 | 205th | 2B Orlando Hudson LAD |
| 19 | 228th | 3B Kevin Kouzmanoff Oak |
| 20 | 229th | C John Baker Fla |
| 21 | 252nd | OF Chris Duncan Was |
| 22 | 253rd | SP John Smoltz Hou |
| 23 | 276th | DH Travis Hafner Cle |
| 24 | 277th | OF Travis Snider Tor |
| 25 | 300th | 2B Alexi Casilla Min |
| 26 | 301st | SP Carl Pavano Min |
| 27 | 324th | 1B Ryan Garko SF |
| 28 | 325th | OF Jerry Hairston Jr. NYA |
| 29 | 348th | SP Dana Eveland Oak |