| Round | Overall | Player |
|---|---|---|
| 1 | 7th | 1B Jeff Bagwell Hou |
| 2 | 18th | OF Shawn Green LA |
| 3 | 31st | RP Armando Benitez NYN |
| 4 | 42nd | 1B Jim Thome Cle |
| 5 | 55th | RP Robb Nen SF |
| 6 | 66th | OF J.D. Drew StL |
| 7 | 79th | 2B Ray Durham ChA |
| 8 | 90th | SP Wade Miller Hou |
| 9 | 103rd | SP Brad Penny Fla |
| 10 | 114th | SP Russ Ortiz SF |
| 11 | 127th | OF Richard Hidalgo Hou |
| 12 | 138th | RP Danny Graves Cin |
| 13 | 151st | C Charles Johnson Fla |
| 14 | 162nd | SP Kazuhisa Ishii LA |
| 15 | 175th | SP Shane Reynolds Hou |
| 16 | 186th | 3B Dean Palmer Det |
| 17 | 199th | OF Bob Higginson Det |
| 18 | 210th | SP Scott Erickson Bal |
| 19 | 223rd | SS Barry Larkin Cin |
| 20 | 234th | 3B Vinny Castilla Atl |
| 21 | 247th | 1B Doug Mientkiewicz Min |
| 22 | 258th | SS Neifi Perez KC |
| 23 | 271st | RP Roberto Hernandez KC |
| 24 | 282nd | OF Gabe Kapler Tex |
| 25 | 295th | C A.J. Pierzynski Min |
| 26 | 306th | SP Jason Marquis Atl |
| 27 | 319th | SP Kenny Rogers Tex |
| 28 | 330th | 2B Jose Macias Det |
| 29 | 343rd | SP Garrett Stephenson StL |