| Round | Overall | Player |
|---|---|---|
| 1 | 7th | 1B Ryan Howard Phi |
| 2 | 18th | SP Roy Halladay Phi |
| 3 | 31st | SS Derek Jeter NYA |
| 4 | 42nd | OF Jason Bay NYN |
| 5 | 55th | SP Matt Cain SF |
| 6 | 66th | RP Brian Wilson SF |
| 7 | 79th | OF Adam Jones Bal |
| 8 | 90th | DH Jorge Posada NYA |
| 9 | 103rd | OF Johnny Damon Det |
| 10 | 114th | RP Bobby Jenks Bos |
| 11 | 127th | 2B Rickie Weeks Mil |
| 12 | 138th | 3B Casey Blake LAD |
| 13 | 151st | SP Clay Buchholz Bos |
| 14 | 162nd | OF Ryan Ludwick SD |
| 15 | 175th | SP Andy Pettitte NYA |
| 16 | 186th | 3B Casey Mcgehee Mil |
| 17 | 199th | OF Xavier Nady Ari |
| 18 | 210th | SP Jonathan Sanchez SF |
| 19 | 223rd | 2B Felipe Lopez STL |
| 20 | 234th | C Jesus Flores Was |
| 21 | 247th | SP Scott Feldman Tex |
| 22 | 258th | 1B Aubrey Huff SF |
| 23 | 271st | SP Ross Ohlendorf Pit |
| 24 | 282nd | SS Cliff Pennington Oak |
| 25 | 295th | SP Vicente Padilla LAD |
| 26 | 306th | OF Mike Cameron Bos |
| 27 | 319th | RP Kerry Wood NYA |
| 28 | 330th | 2B Luis Valbuena Cle |
| 29 | 343rd | SP Brad Bergesen Bal |