| Round | Overall | Player |
|---|---|---|
| 1 | 3rd | 1B David Ortiz Bos |
| 2 | 22nd | OF Andruw Jones Atl |
| 3 | 27th | OF Vernon Wells Tor |
| 4 | 46th | RP Billy Wagner NYN |
| 5 | 51st | RP Trevor Hoffman SD |
| 6 | 70th | OF Pat Burrell Phi |
| 7 | 75th | SP Dontrelle Willis Det |
| 8 | 94th | OF Jeff Francoeur Atl |
| 9 | 99th | SP Adam Wainwright StL |
| 10 | 118th | 3B Adrian Beltre Sea |
| 11 | 123rd | SP Derek Lowe LAD |
| 12 | 142nd | SS Felipe Lopez Was |
| 13 | 147th | SP Tom Glavine Atl |
| 14 | 166th | SP Zach Duke Pit |
| 15 | 171st | 1B Lyle Overbay Tor |
| 16 | 190th | SS Jhonny Peralta Cle |
| 17 | 195th | SP Doug Davis Ari |
| 18 | 214th | SP Roger Clemens NYA |
| 19 | 219th | C Jason Varitek Bos |
| 20 | 238th | SP Noah Lowry SF |
| 21 | 243rd | RP Ryan Dempster ChN |
| 22 | 262nd | OF Matt Kemp LAD |
| 23 | 267th | OF Mike Cameron SD |
| 24 | 286th | OF Melvin Upton TB |
| 25 | 291st | SP Daniel Cabrera Bal |
| 26 | 310th | C Miguel Montero Ari |
| 27 | 315th | 2B Mark Loretta Hou |
| 28 | 334th | SS Brandon Wood LAA |
| 29 | 339th | SP Matt Morris Pit |