1st(1st leg) FK Pelister - CS Hobscheid 3:1 (0:1)
2nd (2nd leg) CS Hobscheid - FK Pelister 0:1 (0:0)
1st(1st leg): 17/06/2000 2nd (2nd leg): 24/06/2000 Winner: FK Pelister
1st(1st leg) Ozeta Dukla Trencin - FC Dinaburg 0:3 dec.
2nd (2nd leg) FC Dinaburg - Ozeta Dukla Trencin 1:0 (1:0)
1st(1st leg): 17/06/2000 2nd (2nd leg): 24/06/2000 Winner: FC Dinaburg
1st(1st leg) Zagłębie Lubin - FK Vilash 4:0 (2:0)
2nd (2nd leg) FK Vilash - Zagłębie Lubin 1:3 (0:1)
1st(1st leg): 17/06/2000 2nd (2nd leg): 24/06/2000 Winner: Zagłębie Lubin
1st(1st leg) HNK Cibalia - FK Obilić 3:1 (2:1)
2nd (2nd leg) FK Obilić - HNK Cibalia 1:1 (1:0)
1st(1st leg): 17/06/2000 2nd (2nd leg): 24/06/2000 Winner: HNK Cibalia
1st(1st leg) Nea Salamina - FK Vllaznia 4:1 (2:0)
2nd (2nd leg) FK Vllaznia - Nea Salamina 1:2 (0:0)
1st(1st leg): 17/06/2000 2nd (2nd leg): 24/06/2000 Winner: Nea Salamina
1st(1st leg) Glenavon FC - Slaven Belupo 1:1 (0:0)
2nd (2nd leg) Slaven Belupo - Glenavon FC 3:0 (2:0)
1st(1st leg): 17/06/2000 2nd (2nd leg): 24/06/2000 Winner: Slaven Belupo
1st(1st leg) Dnepr Mogilev - Silkeborg IF 2:1 (1:1)
2nd (2nd leg) Silkeborg IF - Dnepr Mogilev 1:2 (1:0)
1st(1st leg): 17/06/2000 2nd (2nd leg): 24/06/2000 Winner: Dnepr Mogilev
1st(1st leg) Floriana FC - Stabæk IF 1:1 (1:0)
2nd (2nd leg) Stabæk IF - Floriana FC 2:0 (0:0)
1st(1st leg): 17/06/2000 2nd (2nd leg): 24/06/2000 Winner: Stabæk IF
1st(1st leg) NK Primorje - KVC Westerlo 5:0 (2:0)
2nd (2nd leg) KVC Westerlo - NK Primorje 0:6 (0:4)
1st(1st leg): 17/06/2000 2nd (2nd leg): 24/06/2000 Winner: NK Primorje
1st(1st leg) LASK Linz - Hapoel Petach-Tikva 3:0 dec.
2nd (2nd leg) Hapoel Petach-Tikva - LASK Linz 1:1 (0:1)
1st(1st leg): 18/06/2000 2nd (2nd leg): 24/06/2000 Winner: LASK Linz
1st(1st leg) HB Tórshavn - Lombard FC Tatabanya 0:4 (0:3)
2nd (2nd leg) Lombard FC Tatabanya - HB Tórshavn 3:0 (1:0)
1st(1st leg): 18/06/2000 2nd (2nd leg): 24/06/2000 Winner: Lombard FC Tatabanya
1st(1st leg) ÍF Leiftur - FC Luzern 2:2 (1:0)
2nd (2nd leg) FC Luzern - ÍF Leiftur 4:4 (0:1)
1st(1st leg): 18/06/2000 2nd (2nd leg): 24/06/2000 Winner: ÍF Leiftur
1st(1st leg) Dinamo Tbilisi - Standard Liège 2:2 (2:0)
2nd (2nd leg) Standard Liège - Dinamo Tbilisi 1:1 (0:1)
1st(1st leg): 18/06/2000 2nd (2nd leg): 24/06/2000 Winner: Standard Liège
1st(1st leg) JK Narva Trans - Ceahlăul Piatra Neamt 2:5 (1:2)
2nd (2nd leg) Ceahlăul Piatra Neamt - JK Narva Trans 4:2 (3:1)
1st(1st leg): 18/06/2000 2nd (2nd leg): 24/06/2000 Winner: Ceahlăul Piatra Neamt
1st(1st leg) Cwmbran Town - Nistru Otaci 0:1 (0:0)
2nd (2nd leg) Nistru Otaci - Cwmbran Town 1:0 (0:0)
1st(1st leg): 18/06/2000 2nd (2nd leg): 25/06/2000 Winner: Nistru Otaci
1st(1st leg) Kocaelispor - FK Atlantas 0:1 (0:1)
2nd (2nd leg) FK Atlantas - Kocaelispor 5:3 (0:1, 0:1, 0:1) pso
1st(1st leg): 18/06/2000 2nd (2nd leg): 25/06/2000 Winner: FK Atlantas
1st(1st leg) Västra Frölunda - Zrinjski Mostar 1:0 (0:0)
2nd (2nd leg) Zrinjski Mostar - Västra Frölunda 2:1 (1:0, 1:0) aet
1st(1st leg): 18/06/2000 2nd (2nd leg): 25/06/2000 Winner: Västra Frölunda
1st(1st leg) MyPa Anjalankoski - Neuchâtel Xamax FC 1:2 (1:0)
2nd (2nd leg) Neuchâtel Xamax FC - MyPa Anjalankoski 3:3 (2:0)
1st(1st leg): 18/06/2000 2nd (2nd leg): 25/06/2000 Winner: Neuchâtel Xamax FC
1st(1st leg) Araks Ararat - Sigma Olomouc 1:2 (0:2)
2nd (2nd leg) Sigma Olomouc - Araks Ararat 1:0 (0:0)
1st(1st leg): 18/06/2000 2nd (2nd leg): 25/06/2000 Winner: Sigma Olomouc
1st(1st leg) UC Dublin - FC Velbazhd 1919 Kyustendil 3:3 (1:2)
2nd (2nd leg) FC Velbazhd 1919 Kyustendil - UC Dublin 0:0 (0:0)
1st(1st leg): 18/06/2000 2nd (2nd leg): 25/06/2000 Winner: FC Velbazhd 1919 Kyustendil