| Round | Overall | Player |
|---|---|---|
| 1 | 3rd | SS Derek Jeter NYA |
| 2 | 22nd | OF Juan Gonzalez Det |
| 3 | 27th | 3B Scott Rolen Phi |
| 4 | 46th | SP Orlando Hernandez NYA |
| 5 | 51st | RP Matt Mantei Ari |
| 6 | 70th | SP Roger Clemens NYA |
| 7 | 75th | RP Robb Nen SF |
| 8 | 94th | 1B Andres Galarraga Atl |
| 9 | 99th | RP Mike Jackson Phi |
| 10 | 118th | OF Ben Grieve Oak |
| 11 | 123rd | OF Jeffrey Hammonds Col |
| 12 | 142nd | SP Brad Radke Min |
| 13 | 147th | 2B Eric Young ChN |
| 14 | 166th | SP Rick Reed NYN |
| 15 | 171st | SP Dave Burba Cle |
| 16 | 190th | SP Jon Lieber ChN |
| 17 | 195th | OF Trot Nixon Bos |
| 18 | 214th | SP Steve Woodard Mil |
| 19 | 219th | 1B Ryan Klesko SD |
| 20 | 238th | OF Steve Finley Ari |
| 21 | 243rd | DH Robert Fick Det |
| 22 | 262nd | 3B Mike Lowell Fla |
| 23 | 267th | 2B Todd Walker Min |
| 24 | 286th | C Chris Widger Mon |
| 25 | 291st | SP Kelvim Escobar Tor |
| 26 | 310th | SP Steve Trachsel TB |
| 27 | 315th | C Bobby Estalella SF |