| Round | Overall | Player |
|---|---|---|
| 1 | 4th | 3B David Wright NYN |
| 2 | 21st | 1B Lance Berkman Hou |
| 3 | 28th | C Victor Martinez Cle |
| 4 | 45th | SP Roy Oswalt Hou |
| 5 | 52nd | SP Roy Halladay Tor |
| 6 | 69th | OF Josh Hamilton Tex |
| 7 | 76th | OF Vernon Wells Tor |
| 8 | 93rd | SS Edgar Renteria Det |
| 9 | 100th | SP James Shields TB |
| 10 | 117th | OF Pat Burrell TB |
| 11 | 124th | SP Adam Wainwright StL |
| 12 | 141st | 2B Howie Kendrick LAA |
| 13 | 148th | 1B Nick Johnson Was |
| 14 | 165th | SP Ian Snell Pit |
| 15 | 172nd | SP Matt Garza TB |
| 16 | 189th | SP Ian Kennedy NYA |
| 17 | 196th | SP Jake Westbrook Cle |
| 18 | 213th | OF J.D. Drew Bos |
| 19 | 220th | 2B Akinori Iwamura TB |
| 20 | 237th | SP Jeremy Guthrie Bal |
| 21 | 244th | 3B Melvin Mora Bal |
| 22 | 261st | 1B Daric Barton Oak |
| 23 | 268th | RP Troy Percival TB |
| 24 | 285th | SP Boof Bonser Min |
| 25 | 292nd | SP Joe Saunders LAA |
| 26 | 309th | C Dioner Navarro TB |
| 27 | 316th | SS Cristian Guzman Was |
| 28 | 333rd | OF Cliff Floyd SD |
| 29 | 340th | RP Brian Wilson SF |