| Round | Overall | Player |
|---|---|---|
| 1 | 9th | 2B Roberto Alomar NYN |
| 2 | 16th | SS Derek Jeter NYA |
| 3 | 33rd | 3B Scott Rolen Phi |
| 4 | 40th | SP Mark Mulder Oak |
| 5 | 57th | OF J.D. Drew StL |
| 6 | 64th | RP Robb Nen SF |
| 7 | 81st | 1B Mo Vaughn NYN |
| 8 | 88th | SP Darryl Kile StL |
| 9 | 105th | SP Brad Radke Min |
| 10 | 112th | C Javy Lopez Atl |
| 11 | 129th | 1B Carlos Pena Oak |
| 12 | 136th | 1B Fred McGriff ChN |
| 13 | 153rd | SP Kyle Farnsworth ChN |
| 14 | 160th | SP Chris Carpenter Tor |
| 15 | 177th | OF Juan Pierre Col |
| 16 | 184th | OF Kenny Lofton ChA |
| 17 | 201st | SP Brandon Duckworth Phi |
| 18 | 208th | SP Kris Benson Pit |
| 19 | 225th | SP Kevin Appier Ana |
| 20 | 232nd | SP Andy Ashby LA |
| 21 | 249th | OF Terrence Long Oak |
| 22 | 256th | SS Felipe Lopez Tor |
| 23 | 273rd | 3B Joe Randa KC |
| 24 | 280th | 2B Luis Rivas Min |
| 25 | 297th | SP Jon Garland ChA |
| 26 | 304th | OF Chuck Knoblauch KC |
| 27 | 321st | SP Brett Myers Phi |
| 28 | 328th | OF Milton Bradley Cle |
| 29 | 345th | C Michael Barrett Mon |