| Round | Overall | Player |
|---|---|---|
| 1 | 3rd | SS Miguel Tejada Bal |
| 2 | 22nd | 1B Todd Helton Col |
| 3 | 27th | SP Roy Oswalt Hou |
| 4 | 46th | OF Barry Bonds SF |
| 5 | 51st | 3B Chipper Jones Atl |
| 6 | 70th | RP Brad Lidge Hou |
| 7 | 75th | OF Jim Edmonds StL |
| 8 | 94th | SP Barry Zito Oak |
| 9 | 99th | C Ivan Rodriguez Det |
| 10 | 118th | DH Jim Thome ChA |
| 11 | 123rd | SP Zach Duke Pit |
| 12 | 142nd | SP A.J. Burnett Tor |
| 13 | 147th | SP Freddy Garcia ChA |
| 14 | 166th | 2B Mark Loretta Bos |
| 15 | 171st | OF Jeremy Hermida Fla |
| 16 | 190th | RP Armando Benitez SF |
| 17 | 195th | OF Geoff Jenkins Mil |
| 18 | 214th | SP Brad Penny LAD |
| 19 | 219th | OF Matt Murton ChN |
| 20 | 238th | 2B Mark Ellis Oak |
| 21 | 243rd | SP Chris Young SD |
| 22 | 262nd | SP Carlos Silva Min |
| 23 | 267th | SP Paul Byrd Cle |
| 24 | 286th | RP Chris Ray Bal |
| 25 | 291st | 1B Adam LaRoche Pit |
| 26 | 310th | 3B Tony Batista Min |
| 27 | 315th | C Ryan Doumit Pit |
| 28 | 334th | SP Jamie Moyer Phi |
| 29 | 339th | SS Alex Gonzalez Bos |