| Round | Overall | Player |
|---|---|---|
| 1 | 2nd | 1B Todd Helton Col |
| 2 | 23rd | OF Larry Walker Col |
| 3 | 26th | OF Lance Berkman Hou |
| 4 | 47th | 1B Phil Nevin SD |
| 5 | 50th | OF Adam Dunn Cin |
| 6 | 71st | 3B Aramis Ramirez Pit |
| 7 | 74th | SP Josh Beckett Fla |
| 8 | 95th | 2B Craig Biggio Hou |
| 9 | 98th | OF Jim Edmonds StL |
| 10 | 119th | OF Richard Hidalgo Hou |
| 11 | 122nd | 3B Hank Blalock Tex |
| 12 | 143rd | C Toby Hall TB |
| 13 | 146th | SP Brad Penny Fla |
| 14 | 167th | SP Rick Reed Min |
| 15 | 170th | C Charles Johnson Fla |
| 16 | 191st | SP Livan Hernandez SF |
| 17 | 194th | SS Alex Gonzalez ChN |
| 18 | 215th | SP Ramon Ortiz Ana |
| 19 | 218th | 1B Kevin Young Pit |
| 20 | 239th | SP Orlando Hernandez NYA |
| 21 | 242nd | SP Scott Schoeneweis Ana |
| 22 | 263rd | SS Omar Vizquel Cle |
| 23 | 266th | SP Carl Pavano Mon |
| 24 | 287th | SP Jamey Wright Mil |
| 25 | 290th | SP Bobby J. Jones SD |
| 26 | 311th | 2B Frank Menechino Oak |
| 27 | 314th | SP Ismael Valdez Tex |
| 28 | 335th | OF Jeff Conine Bal |
| 29 | 338th | SP Ryan Drese Cle |