* = Lefty, + = Switch
| Pick | Manager | Player | From Team | Notes |
| Picks 1 through 32: No more than 2 players from any existing team | ||||
| Players cannot be ranked 1 to 8, they must be 9 or lower. | ||||
| 1 | Ralph | Leiter,A* | CAL GE | |
| 2 | Mike | Burkett,J | CIN SS | |
| 3 | Chris | Lidle,C | SFE DM | |
| 4 | Bob | Guzman,C+ | SFE DM | SFE DM reaches limit |
| 5 | Bob | Penny,B | SSB PV | |
| 6 | Chris | Hidalgo,R | LAV RW | |
| 7 | Mike | Kile,D | DAR JC | |
| 8 | Ralph | Soriano,A | CIN SS | CIN SS reaches limit |
| 9 | Ralph | Mondesi,R | DAR JC | DAR JC reaches limit |
| 10 | Mike | Ramirez,A | CPK PP | |
| 11 | Chris | Durham,R+ | HIP BD | |
| 12 | Bob | Griffey Jr.,K* | SSB PV | SSB PV reaches limit |
| 13 | Bob | Sexson,R | CPK PP | CPK PP reaches limit |
| 14 | Chris | Grace,M* | CRC AD | |
| 15 | Mike | Biggio,C | CAL GE | CAL GE reaches limit |
| 16 | Ralph | Wagner,B* | CRC AD | CRC AD reaches limit |
| 17 | Ralph | Nomo,H | WRI JS | |
| 18 | Mike | Valentin,J+ | CHI SH | |
| 19 | Chris | Walker,T* | LEW AA | |
| 20 | Bob | Giambi,Jeremy* | COL FL | |
| 21 | Bob | Reed,R | SOB MB | |
| 22 | Chris | Bautista,D | CSW RG | |
| 23 | Mike | Martinez,T* | WRI JS | WRI JS reaches limit |
| 24 | Ralph | Higginson,B* | LAV RW | LAV RW reaches limit |
| 25 | Ralph | Cirillo,J | HIP BD | HIP BD reaches limit |
| 26 | Mike | Lopez,J | DET MW | |
| 27 | Chris | Rios,A* | CHI SH | CHI SH reaches limit |
| 28 | Bob | Mcgriff,F* | SOB MB | SOB MB reaches limit |
| 29 | Bob | Pierzynski,A* | LEW AA | LEW AA reaches limit |
| 30 | Chris | Henderson,R | CSW RG | CSW RG reaches limit |
| 31 | Mike | Jones,J* | DET MW | DET MW reaches limit |
| 32 | Ralph | Castillo,F | COL FL | COL FL reaches limit |
| Next 8 highest ranking players protected by existing teams. | ||||
| Picks 33 through 64: No more than 2 players from any existing team | ||||
| 33 | Bob | Mclemore,M+ | CHI SH | |
| 34 | Chris | Coggin,D | CIN SS | |
| 35 | Mike | Glavine,T* | SOB MB | |
| 36 | Ralph | Nelson,Jeff | CAL GE | |
| 37 | Ralph | Cordova,M | SFE DM | |
| 38 | Mike | Anderson,G* | SFE DM | SFE DM reaches limit |
| 39 | Chris | Wooten,S | LEW AA | |
| 40 | Bob | Sparks,S | CRC AD | |
| 41 | Bob | Menechino,F | CHI SH | CHI SH reaches limit |
| 42 | Chris | Alfonseca,A | LEW AA | LEW AA reaches limit |
| 43 | Mike | Van Poppel,T | CAL GE | CAL GE reaches limit |
| 44 | Ralph | Fick,R* | CPK PP | |
| 45 | Ralph | Appier,K | CPK PP | CPK PP reaches limit |
| 46 | Mike | Lowe,S | LAV RW | |
| 47 | Chris | Schmidt,J | DAR JC | |
| 48 | Bob | Ventura,R* | CRC AD | CRC AD reaches limit |
| 49 | Bob | Mendoza,R | HIP BD | |
| 50 | Chris | Hollandsworth,T* | COL FL | |
| 51 | Mike | Reynolds,S | HIP BD | HIP BD reaches limit |
| 52 | Ralph | Sullivan,S | LAV RW | LAV RW reaches limit |
| 53 | Ralph | Graffanino,T | SOB MB | SOB MB reaches limit |
| 54 | Mike | Levine,A | DET MW | |
| 55 | Chris | Miller,D | CSW RG | |
| 56 | Bob | Lankford,R* | CIN SS | CIN SS reaches limit |
| 57 | Bob | Eaton,A | DET MW | DET MW reaches limit |
| 58 | Chris | Hernandez,J | CSW RG | CSW RG reaches limit |
| 59 | Mike | Koch,B | SSB PV | |
| 60 | Ralph | Christiansen,J* | DAR JC | DAR JC reaches limit |
| 61 | Ralph | Macias,J+ | COL FL | COL FL reaches limit |
| 62 | Mike | Segui,D+ | SSB PV | SSB PV reaches limit |
| 63 | Chris | Quantrill,P | WRI JS | |
| 64 | Bob | Ausmus,B | WRI JS | WRI JS reaches limit |
| Next 4 highest ranking players protected by existing teams. | ||||
| Picks 65 through 100: Any number of players from any team from the available list | ||||
| 65 | Ralph | Lee,T* | CRC AD | |
| 66 | Mike | Shaw,J | SOB MB | |
| 67 | Chris | Castilla,V | CSW RG | |
| 68 | Bob | Charlton,N* | CHI SH | |
| 69 | Bob | Glanville,D | CRC AD | |
| 70 | Chris | Darensbourg,V* | CIN SS | |
| 71 | Mike | Jenkins,G* | LAV RW | |
| 72 | Ralph | Halladay,R | CPK PP | |
| 73 | Ralph | Remlinger,M* | SOB MB | |
| 74 | Mike | Carpenter,C | LEW AA | |
| 75 | Chris | Jimenez,D+ | CHI SH | |
| 76 | Bob | Reese,P | HIP BD | |
| 77 | Bob | Gordon,T | DET MW | |
| 78 | Chris | Lofton,K* | CPK PP | |
| 79 | Mike | Long,T* | LEW AA | |
| 80 | Ralph | Girardi,J | CAL GE | |
| 81 | Ralph | O'neill,P* | LAV RW | |
| 82 | Mike | Fryman,T | LEW AA | |
| 83 | Chris | Hawkins,L | WRI JS | |
| 84 | Bob | King,R* | DET MW | |
| 85 | Bob | Herges,M | DET MW | |
| 86 | Chris | Abbott,P | CSW RG | |
| 87 | Mike | Lugo,J | LEW AA | |
| 88 | Ralph | Loretta,M | CSW RG | |
| 89 | Ralph | Young,K | SFE DM | |
| 90 | Mike | Hatteberg,S* | COL FL | |
| 91 | Chris | Borbon,P* | DET MW | |
| 92 | Bob | Ibanez,R* | CHI SH | |
| 93 | Bob | Cruz,N | CRC AD | |
| 94 | Chris | Stanton,M* | SOB MB | |
| 95 | Mike | Smith,B* | DAR JC | |
| 96 | Ralph | Daal,O* | SOB MB | |
| 97 | Ralph | Branyan,R* | CSW RG | |
| 98 | Mike | Lewis,D | SOB MB | |
| 99 | Chris | Tapani,K | DET MW | |
| 100 | Bob | Baez,D | SSB PV | |