| Round | Overall | Player |
|---|---|---|
| 1 | 3rd | OF Vladimir Guerrero LAA |
| 2 | 22nd | SP Pedro Martinez NYN |
| 3 | 27th | SS Derek Jeter NYA |
| 4 | 46th | SP Ben Sheets Mil |
| 5 | 51st | OF Vernon Wells Tor |
| 6 | 70th | SP Oliver Perez Pit |
| 7 | 75th | C Jorge Posada NYA |
| 8 | 94th | SP Kerry Wood ChN |
| 9 | 99th | 1B Justin Morneau Min |
| 10 | 118th | SP Javier Vazquez Ari |
| 11 | 123rd | OF Ken Griffey Jr Cin |
| 12 | 142nd | 2B Jose Vidro Was |
| 13 | 147th | SP Brad Penny LAD |
| 14 | 166th | SP Wade Miller Bos |
| 15 | 171st | SP David Wells Bos |
| 16 | 190th | 3B Bill Mueller Bos |
| 17 | 195th | OF Torii Hunter Min |
| 18 | 214th | OF Mike Cameron NYN |
| 19 | 219th | OF Shannon Stewart Min |
| 20 | 238th | SP Steve Trachsel NYN |
| 21 | 243rd | OF Bernie Williams NYA |
| 22 | 262nd | 3B Jose Valentin LAD |
| 23 | 267th | 2B Junior Spivey Was |
| 24 | 286th | DH Josh Phelps TB |
| 25 | 291st | SS Cristian Guzman Was |
| 26 | 310th | C J.D. Closser Col |
| 27 | 315th | OF Rocco Baldelli TB |
| 28 | 334th | SP Brett Tomko SF |
| 29 | 339th | SP Jose Lima KC |