| Round | Overall | Player |
|---|---|---|
| 1 | 8th | OF Barry Bonds SF |
| 2 | 17th | C Ivan Rodriguez Tex |
| 3 | 32nd | SS Derek Jeter NYA |
| 4 | 41st | 1B Jim Thome Cle |
| 5 | 56th | OF Jay Buhner Sea |
| 6 | 65th | 3B Scott Rolen Phi |
| 7 | 80th | P Jeff Fassero Sea |
| 8 | 89th | P John Franco NYN |
| 9 | 104th | 2B Damion Easley Det |
| 10 | 113th | P Bobby J. Jones NYN |
| 11 | 128th | P Doug Jones Mil |
| 12 | 137th | P Dennis Eckersley Bos |
| 13 | 152nd | OF Derek Bell Hou |
| 14 | 161st | P Matt Morris StL |
| 15 | 176th | OF Bernard Gilkey NYN |
| 16 | 185th | P Rich Loiselle Pit |
| 17 | 200th | P Bobby Witt Tex |
| 18 | 209th | C Jeff Reed Col |
| 19 | 224th | 1B Jeff King KC |
| 20 | 233rd | P Scott Kamieniecki Bal |
| 21 | 248th | P James Baldwin ChA |
| 22 | 257th | 3B Ron Coomer Min |
| 23 | 272nd | OF Otis Nixon Min |
| 24 | 281st | P Roger Pavlik Tex |
| 25 | 296th | P Doug Drabek Bal |
| 26 | 305th | P Woody Williams Tor |
| 27 | 320th | P Dave Mlicki NYN |