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| 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 | ||||
