| Round | Overall | Player |
|---|---|---|
| 1 | 7th | SS Hanley Ramirez Fla |
| 2 | 18th | SS Jimmy Rollins Phi |
| 3 | 31st | OF Carlos Beltran NYN |
| 4 | 42nd | 3B Garrett Atkins Col |
| 5 | 55th | OF Bobby Abreu NYA |
| 6 | 66th | 3B Chipper Jones Atl |
| 7 | 79th | DH Jim Thome ChA |
| 8 | 90th | SP John Smoltz Bos |
| 9 | 103rd | SP Brett Myers Phi |
| 10 | 114th | SP Francisco Liriano Min |
| 11 | 127th | 2B Rickie Weeks Mil |
| 12 | 138th | SP Tim Lincecum Hou |
| 13 | 151st | 1B James Loney LAD |
| 14 | 162nd | RP Francisco Cordero Cin |
| 15 | 175th | RP Jason Isringhausen StL |
| 16 | 186th | SP Andy Pettitte NYA |
| 17 | 199th | OF Jeremy Hermida Fla |
| 18 | 210th | 1B Joey Votto Cin |
| 19 | 223rd | SP Jon Lester Bos |
| 20 | 234th | SP Joba Chamberlain NYA |
| 21 | 247th | RP B.J. Ryan Tor |
| 22 | 258th | OF Gary Matthews Jr. LAA |
| 23 | 271st | SP Kenny Rogers Det |
| 24 | 282nd | SP Nate Robertson Det |
| 25 | 295th | C Yorvit Torrealba Col |
| 26 | 306th | SP Jamie Moyer Phi |
| 27 | 319th | C John Buck KC |
| 28 | 330th | 3B Josh Fields ChA |
| 29 | 343rd | SP Homer Bailey Cin |