| Round | Overall | Player |
|---|---|---|
| 1 | 1st | SS Alex Rodriguez Tex |
| 2 | 24th | OF Shawn Green LA |
| 3 | 25th | 3B Scott Rolen StL |
| 4 | 48th | SP Mark Prior ChN |
| 5 | 49th | 1B Rafael Palmeiro Tex |
| 6 | 72nd | RP Eddie Guardado Min |
| 7 | 73rd | C Paul Lo Duca LA |
| 8 | 96th | OF Hideki Matsui NYA |
| 9 | 97th | SP A.J. Burnett Fla |
| 10 | 120th | OF Jacque Jones Min |
| 11 | 121st | SP Kevin Brown LA |
| 12 | 144th | 2B Brandon Phillips Cle |
| 13 | 145th | SP Woody Williams StL |
| 14 | 168th | SP Ted Lilly Oak |
| 15 | 169th | SP Oliver Perez SD |
| 16 | 192nd | 1B Fred McGriff LA |
| 17 | 193rd | 1B Carlos Pena Det |
| 18 | 216th | RP Mike DeJean StL |
| 19 | 217th | SP Danny Graves Cin |
| 20 | 240th | OF Kevin Millar Bos |
| 21 | 241st | SP Paul Byrd Atl |
| 22 | 264th | 3B Jeff Cirillo Sea |
| 23 | 265th | C Ben Davis Sea |
| 24 | 288th | SS Julio Lugo TB |
| 25 | 289th | 2B Mike Young Tex |
| 26 | 312th | SP Omar Daal Bal |
| 27 | 313th | OF Joe Borchard ChA |
| 28 | 336th | OF Reggie Sanders Pit |
| 29 | 337th | C Josh Paul ChN |