| Round | Overall | Player |
|---|---|---|
| 1 | 1st | 3B Alex Rodriguez NYA |
| 2 | 24th | 1B Mark Teixeira NYA |
| 3 | 25th | C Victor Martinez Cle |
| 4 | 48th | 2B Robinson Cano NYA |
| 5 | 49th | C Brian McCann Atl |
| 6 | 72nd | OF Vernon Wells Tor |
| 7 | 73rd | RP Billy Wagner NYN |
| 8 | 96th | OF Jeff Francoeur Atl |
| 9 | 97th | SS J.J. Hardy Mil |
| 10 | 120th | OF Jermaine Dye ChA |
| 11 | 121st | SP Chien-Ming Wang NYA |
| 12 | 144th | SP Jeff Francis Col |
| 13 | 145th | SP Scott Kazmir TB |
| 14 | 168th | SS Khalil Greene SD |
| 15 | 169th | RP Joakim Soria KC |
| 16 | 192nd | OF Josh Willingham Fla |
| 17 | 193rd | RP Jason Isringhausen StL |
| 18 | 216th | 2B Aaron Hill Tor |
| 19 | 217th | SP Jon Garland Ari |
| 20 | 240th | OF Lastings Milledge Was |
| 21 | 241st | 3B Scott Rolen Tor |
| 22 | 264th | SP Tom Glavine Atl |
| 23 | 265th | 1B Jason Giambi Oak |
| 24 | 288th | SP Andrew Miller Fla |
| 25 | 289th | SP Brian Bannister KC |
| 26 | 312th | C John Buck KC |
| 27 | 313th | SP Kevin Slowey Min |
| 28 | 336th | SP Mark Mulder StL |
| 29 | 337th | 2B Jayson Nix Col |