1st(1st leg) Rapid Wien - Valletta FC 3:0 (0:0)
2nd (2nd leg) Valletta FC - Rapid Wien 0:2 (0:0)
1st(1st leg): 28/07/1999 15:00 2nd (2nd leg): 04/08/1999 17:00 Winner: Rapid Wien
1st(1st leg) Dinamo Tbilisi - FC Zimbru 2:1 (0:0)
2nd (2nd leg) FC Zimbru - Dinamo Tbilisi 2:0 (1:0)
1st(1st leg): 28/07/1999 15:00 2nd (2nd leg): 04/08/1999 16:00 Winner: FC Zimbru
1st(1st leg) Rapid Bucureşti - Skonto FC 3:3 (1:2)
2nd (2nd leg) Skonto FC - Rapid Bucureşti 2:1 (0:1)
1st(1st leg): 28/07/1999 15:30 2nd (2nd leg): 04/08/1999 19:00 Winner: Skonto FC
1st(1st leg) Dnepr Mogilev - AIK Solna 0:1 (0:0)
2nd (2nd leg) AIK Solna - Dnepr Mogilev 2:0 (0:0)
1st(1st leg): 28/07/1999 16:00 2nd (2nd leg): 04/08/1999 18:00 Winner: AIK Solna
1st(1st leg) Anorthosis Famagusta - Slovan Bratislava 2:1 (1:0)
2nd (2nd leg) Slovan Bratislava - Anorthosis Famagusta 1:1 (0:0)
1st(1st leg): 28/07/1999 16:30 2nd (2nd leg): 04/08/1999 17:00 Winner: Anorthosis Famagusta
1st(1st leg) PFC Litex Lovech - Widzew Łódź 4:1 (1:0)
2nd (2nd leg) Widzew Łódź - PFC Litex Lovech 3:2 (1:1, 4:1, 4:1) pso
1st(1st leg): 28/07/1999 16:30 2nd (2nd leg): 04/08/1999 19:15 Winner: Widzew Łódź
1st(1st leg) CSKA Moskva - Molde FK 2:0 (1:0)
2nd (2nd leg) Molde FK - CSKA Moskva 4:0 (0:0)
1st(1st leg): 28/07/1999 17:00 2nd (2nd leg): 04/08/1999 17:00 Winner: Molde FK
1st(1st leg) Haka Valkeakoski - Rangers FC 1:4 (0:3)
2nd (2nd leg) Rangers FC - Haka Valkeakoski 3:0 (2:0)
1st(1st leg): 28/07/1999 17:00 2nd (2nd leg): 04/08/1999 19:45 Winner: Rangers FC
1st(1st leg) Dinamo Kiev - FK Zalgiris 2:0 (1:0)
2nd (2nd leg) FK Zalgiris - Dinamo Kiev 0:1 (0:1)
1st(1st leg): 28/07/1999 17:00 2nd (2nd leg): 04/08/1999 16:00 Winner: Dinamo Kiev
1st(1st leg) Beşiktaş - Hapoel Haifa 1:1 (0:0)
2nd (2nd leg) Hapoel Haifa - Beşiktaş 0:0 (0:0)
1st(1st leg): 28/07/1999 18:45 2nd (2nd leg): 04/08/1999 18:30 Winner: Hapoel Haifa
1st(1st leg) FK Sloga Jugomagnat - Brøndby IF 0:1 (0:1)
2nd (2nd leg) Brøndby IF - FK Sloga Jugomagnat 1:0 (1:0)
1st(1st leg): 28/07/1999 19:00 2nd (2nd leg): 04/08/1999 19:45 Winner: Brøndby IF
1st(1st leg) Maribor Teatanic - KRC Genk 5:1 (1:1)
2nd (2nd leg) KRC Genk - Maribor Teatanic 3:0 (1:0)
1st(1st leg): 28/07/1999 19:00 2nd (2nd leg): 04/08/1999 19:30 Winner: Maribor Teatanic
1st(1st leg) Partizan - HNK Rijeka 3:1 (2:0)
2nd (2nd leg) HNK Rijeka - Partizan 0:3 (0:2)
1st(1st leg): 28/07/1999 19:15 2nd (2nd leg): 04/08/1999 19:30 Winner: Partizan
1st(1st leg) ÍBV Vestmannaeyjar - MTK Hungaria 0:2 (0:1)
2nd (2nd leg) MTK Hungaria - ÍBV Vestmannaeyjar 3:1 (3:0)
1st(1st leg): 28/07/1999 20:00 2nd (2nd leg): 04/08/1999 19:45 Winner: MTK Hungaria