| Round | Overall | Player |
|---|---|---|
| 1 | 9th | SS Jose Reyes NYN |
| 2 | 16th | 1B Mark Teixeira NYA |
| 3 | 33rd | OF Carl Crawford TB |
| 4 | 40th | 1B Derrek Lee ChN |
| 5 | 57th | SP Josh Beckett Bos |
| 6 | 64th | 2B Brian Roberts Bal |
| 7 | 81st | OF Chris Young Ari |
| 8 | 88th | OF Corey Hart Mil |
| 9 | 105th | 3B Adrian Beltre Sea |
| 10 | 112th | SP A.J. Burnett Tor |
| 11 | 129th | SP Yovani Gallardo Mil |
| 12 | 136th | SP Scott Kazmir TB |
| 13 | 153rd | SP Ted Lilly ChN |
| 14 | 160th | RP Huston Street Oak |
| 15 | 177th | C Ivan Rodriguez NYA |
| 16 | 184th | SP Hiroki Kuroda LAD |
| 17 | 201st | RP Joakim Soria KC |
| 18 | 208th | SP Matt Capps Pit |
| 19 | 225th | 1B Conor Jackson Ari |
| 20 | 232nd | OF Josh Willingham Fla |
| 21 | 249th | OF Adam Jones Bal |
| 22 | 256th | SP Chad Gaudin ChN |
| 23 | 273rd | 3B Mark Reynolds Ari |
| 24 | 280th | SP Jair Jurrjens Atl |
| 25 | 297th | SP Ubaldo Jimenez Col |
| 26 | 304th | C A.J. Pierzynski ChA |
| 27 | 321st | SP Scott Baker Min |
| 28 | 328th | 3B Juan Uribe SF |
| 29 | 345th | 2B Freddy Sanchez Pit |