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| U | FC Ararat | - | Sint-Truidense VV | 0:2 (0:2) | ||
| R | Sint-Truidense VV | - | FC Ararat | 3:1 (2:0) | ||
| U: 03.07.1999 15:00 | R: 10.07.1999 20:00 | Winnaars: Sint-Truidense VV | ||||
| U | Qarabağ FK | - | Montpellier HSC | 0:3 (0:3) | ||
| R | Montpellier HSC | - | Qarabağ FK | 6:0 (2:0) | ||
| U: 03.07.1999 16:00 | R: 10.07.1999 20:00 | Winnaars: Montpellier HSC | ||||
| U | FK Ventspils | - | Kocaelispor | 1:1 (0:0) | ||
| R | Kocaelispor | - | FK Ventspils | 2:0 (1:0) | ||
| U: 03.07.1999 17:00 | R: 11.07.1999 17:00 | Winnaars: Kocaelispor | ||||
| U | MŠK Žilina | - | FC Metz | 2:1 (2:0) | ||
| R | FC Metz | - | MŠK Žilina | 3:0 (0:0) | ||
| U: 03.07.1999 17:30 | R: 11.07.1999 18:00 | Winnaars: FC Metz | ||||
| U | Cementarnica Skopje | - | Rostselmash Rostov | 1:1 (1:1) | ||
| R | Rostselmash Rostov | - | Cementarnica Skopje | 2:1 (1:0) | ||
| U: 03.07.1999 18:00 | R: 10.07.1999 17:00 | Winnaars: Rostselmash Rostov | ||||
| U | SK Brann | - | NK Varteks | 3:0 (1:0) | ||
| R | NK Varteks | - | SK Brann | 5:4 (2:0, 3:0, 3:0) d.p. | ||
| U: 03.07.1999 18:00 | R: 10.07.1999 20:00 | Winnaars: NK Varteks | ||||
| U | Neuchâtel Xamax FC | - | Budapesti Vasas | 0:2 (0:2) | ||
| R | Budapesti Vasas | - | Neuchâtel Xamax FC | 1:0 (1:0) | ||
| U: 03.07.1999 19:30 | R: 10.07.1999 20:00 | Winnaars: Budapesti Vasas | ||||
| U | Sporting Lokeren | - | ÍA Akranes | 3:1 (1:0) | ||
| R | ÍA Akranes | - | Sporting Lokeren | 1:3 (1:1) | ||
| U: 03.07.1999 20:00 | R: 11.07.1999 18:00 | Winnaars: Sporting Lokeren | ||||
| U | AC Perugia | - | FK Pobeda | 1:0 (0:0) | ||
| R | FK Pobeda | - | AC Perugia | 0:0 (0:0) | ||
| U: 03.07.1999 20:45 | R: 11.07.1999 17:30 | Winnaars: AC Perugia | ||||
| U | FC Kopenhagen | - | Polonia Warszawa | 0:3 (0:0) | ||
| R | Polonia Warszawa | - | FC Kopenhagen | 1:1 (1:0) | ||
| U: 04.07.1999 14:00 | R: 10.07.1999 16:00 | Winnaars: Polonia Warszawa | ||||
| U | Jokerit Helsinki | - | Floriana FC | 2:1 (1:0) | ||
| R | Floriana FC | - | Jokerit Helsinki | 1:1 (1:0) | ||
| U: 04.07.1999 17:00 | R: 10.07.1999 17:00 | Winnaars: Jokerit Helsinki | ||||
| U | Ceahlăul Piatra Neamt | - | NK Jedinstvo | 2:1 (0:1) | ||
| R | NK Jedinstvo | - | Ceahlăul Piatra Neamt | 1:3 (1:3) | ||
| U: 04.07.1999 17:00 | R: 10.07.1999 18:00 | Winnaars: Ceahlăul Piatra Neamt | ||||
| U | FC Basel | - | FC Boby-sport Brno | 0:0 (0:0) | ||
| R | FC Boby-sport Brno | - | FC Basel | 2:4 (1:2) | ||
| U: 04.07.1999 17:30 | R: 11.07.1999 18:00 | Winnaars: FC Basel | ||||
| U | MSV Duisburg | - | Newry Town FC | 2:0 (0:0) | ||
| R | Newry Town FC | - | MSV Duisburg | 1:0 (1:0) | ||
| U: 04.07.1999 18:00 | R: 10.07.1999 16:00 | Winnaars: MSV Duisburg | ||||
| U | Rudar Velenje | - | Austria Lustenau | 1:2 (0:2) | ||
| R | Austria Lustenau | - | Rudar Velenje | 2:1 (1:1) | ||
| U: 04.07.1999 18:00 | R: 10.07.1999 19:00 | Winnaars: Austria Lustenau | ||||
| U | Hammarby IF | - | FK Gomel | 4:0 (1:0) | ||
| R | FK Gomel | - | Hammarby IF | 2:2 (0:1) | ||
| U: 04.07.1999 18:00 | R: 11.07.1999 17:00 | Winnaars: Hammarby IF | ||||
