1st(1st leg) FC Ararat - Sint-Truidense VV 0:2 (0:2)
2nd (2nd leg) Sint-Truidense VV - FC Ararat 3:1 (2:0)
1st(1st leg): 03/07/1999 14:00 2nd (2nd leg): 10/07/1999 19:00 Winner: Sint-Truidense VV
1st(1st leg) Qarabağ FK - Montpellier HSC 0:3 (0:3)
2nd (2nd leg) Montpellier HSC - Qarabağ FK 6:0 (2:0)
1st(1st leg): 03/07/1999 15:00 2nd (2nd leg): 10/07/1999 19:00 Winner: Montpellier HSC
1st(1st leg) FK Ventspils - Kocaelispor 1:1 (0:0)
2nd (2nd leg) Kocaelispor - FK Ventspils 2:0 (1:0)
1st(1st leg): 03/07/1999 16:00 2nd (2nd leg): 11/07/1999 16:00 Winner: Kocaelispor
1st(1st leg) MŠK Žilina - FC Metz 2:1 (2:0)
2nd (2nd leg) FC Metz - MŠK Žilina 3:0 (0:0)
1st(1st leg): 03/07/1999 16:30 2nd (2nd leg): 11/07/1999 17:00 Winner: FC Metz
1st(1st leg) Cementarnica Skopje - Rostselmash Rostov 1:1 (1:1)
2nd (2nd leg) Rostselmash Rostov - Cementarnica Skopje 2:1 (1:0)
1st(1st leg): 03/07/1999 17:00 2nd (2nd leg): 10/07/1999 16:00 Winner: Rostselmash Rostov
1st(1st leg) SK Brann - NK Varteks 3:0 (1:0)
2nd (2nd leg) NK Varteks - SK Brann 5:4 (2:0, 3:0, 3:0) pso
1st(1st leg): 03/07/1999 17:00 2nd (2nd leg): 10/07/1999 19:00 Winner: NK Varteks
1st(1st leg) Neuchâtel Xamax FC - Budapesti Vasas 0:2 (0:2)
2nd (2nd leg) Budapesti Vasas - Neuchâtel Xamax FC 1:0 (1:0)
1st(1st leg): 03/07/1999 18:30 2nd (2nd leg): 10/07/1999 19:00 Winner: Budapesti Vasas
1st(1st leg) Sporting Lokeren - ÍA Akranes 3:1 (1:0)
2nd (2nd leg) ÍA Akranes - Sporting Lokeren 1:3 (1:1)
1st(1st leg): 03/07/1999 19:00 2nd (2nd leg): 11/07/1999 17:00 Winner: Sporting Lokeren
1st(1st leg) AC Perugia - FK Pobeda 1:0 (0:0)
2nd (2nd leg) FK Pobeda - AC Perugia 0:0 (0:0)
1st(1st leg): 03/07/1999 19:45 2nd (2nd leg): 11/07/1999 16:30 Winner: AC Perugia
1st(1st leg) FC København - Polonia Warszawa 0:3 (0:0)
2nd (2nd leg) Polonia Warszawa - FC København 1:1 (1:0)
1st(1st leg): 04/07/1999 13:00 2nd (2nd leg): 10/07/1999 15:00 Winner: Polonia Warszawa
1st(1st leg) Jokerit Helsinki - Floriana FC 2:1 (1:0)
2nd (2nd leg) Floriana FC - Jokerit Helsinki 1:1 (1:0)
1st(1st leg): 04/07/1999 16:00 2nd (2nd leg): 10/07/1999 16:00 Winner: Jokerit Helsinki
1st(1st leg) Ceahlăul Piatra Neamt - NK Jedinstvo 2:1 (0:1)
2nd (2nd leg) NK Jedinstvo - Ceahlăul Piatra Neamt 1:3 (1:3)
1st(1st leg): 04/07/1999 16:00 2nd (2nd leg): 10/07/1999 17:00 Winner: Ceahlăul Piatra Neamt
1st(1st leg) FC Basel 1893 - FC Boby-sport Brno 0:0 (0:0)
2nd (2nd leg) FC Boby-sport Brno - FC Basel 1893 2:4 (1:2)
1st(1st leg): 04/07/1999 16:30 2nd (2nd leg): 11/07/1999 17:00 Winner: FC Basel 1893
1st(1st leg) MSV Duisburg - Newry Town FC 2:0 (0:0)
2nd (2nd leg) Newry Town FC - MSV Duisburg 1:0 (1:0)
1st(1st leg): 04/07/1999 17:00 2nd (2nd leg): 10/07/1999 15:00 Winner: MSV Duisburg
1st(1st leg) Rudar Velenje - Austria Lustenau 1:2 (0:2)
2nd (2nd leg) Austria Lustenau - Rudar Velenje 2:1 (1:1)
1st(1st leg): 04/07/1999 17:00 2nd (2nd leg): 10/07/1999 18:00 Winner: Austria Lustenau
1st(1st leg) Hammarby IF - FK Gomel 4:0 (1:0)
2nd (2nd leg) FK Gomel - Hammarby IF 2:2 (0:1)
1st(1st leg): 04/07/1999 17:00 2nd (2nd leg): 11/07/1999 16:00 Winner: Hammarby IF