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| 1st(1st leg) | Herfølge BK | - | MŠK Žilina | 0:2 (0:0) | ||
| 2nd (2nd leg) | MŠK Žilina | - | Herfølge BK | 2:0 (1:0) | ||
| 1st(1st leg): 19/06/1999 14:00 | 2nd (2nd leg): 26/06/1999 16:30 | Winner: MŠK Žilina | ||||
| 1st(1st leg) | Vålerenga IF | - | FK Ventspils | 1:0 (0:0) | ||
| 2nd (2nd leg) | FK Ventspils | - | Vålerenga IF | 2:0 (1:0) | ||
| 1st(1st leg): 19/06/1999 15:00 | 2nd (2nd leg): 26/06/1999 16:00 | Winner: FK Ventspils | ||||
| 1st(1st leg) | Polonia Warszawa | - | Tiligul Tiraspol | 4:0 (0:0) | ||
| 2nd (2nd leg) | Tiligul Tiraspol | - | Polonia Warszawa | 0:0 (0:0) | ||
| 1st(1st leg): 19/06/1999 16:00 | 2nd (2nd leg): 26/06/1999 16:00 | Winner: Polonia Warszawa | ||||
| 1st(1st leg) | Spartak Varna | - | Sint-Truidense VV | 1:2 (1:0) | ||
| 2nd (2nd leg) | Sint-Truidense VV | - | Spartak Varna | 6:0 (4:0) | ||
| 1st(1st leg): 19/06/1999 16:00 | 2nd (2nd leg): 26/06/1999 19:00 | Winner: Sint-Truidense VV | ||||
| 1st(1st leg) | FCM Bacău | - | FC Ararat | 0:1 (0:0) | ||
| 2nd (2nd leg) | FC Ararat | - | FCM Bacău | 1:0 (0:0) | ||
| 1st(1st leg): 19/06/1999 16:00 | 2nd (2nd leg): 26/06/1999 14:00 | Winner: FC Ararat | ||||
| 1st(1st leg) | Lokomotiv-96 Vitebsk | - | NK Varteks | 1:2 (0:1) | ||
| 2nd (2nd leg) | NK Varteks | - | Lokomotiv-96 Vitebsk | 2:2 (0:1) | ||
| 1st(1st leg): 19/06/1999 16:00 | 2nd (2nd leg): 26/06/1999 19:00 | Winner: NK Varteks | ||||
| 1st(1st leg) | ÍA Akranes | - | KF Teuta Durrës | 5:1 (3:1) | ||
| 2nd (2nd leg) | KF Teuta Durrës | - | ÍA Akranes | 2:1 (0:1) | ||
| 1st(1st leg): 19/06/1999 17:00 | 2nd (2nd leg): 26/06/1999 17:00 | Winner: ÍA Akranes | ||||
| 1st(1st leg) | Union Luxembourg | - | Budapesti Vasas | 1:3 (0:2) | ||
| 2nd (2nd leg) | Budapesti Vasas | - | Union Luxembourg | 4:0 (1:0) | ||
| 1st(1st leg): 19/06/1999 17:00 | 2nd (2nd leg): 26/06/1999 18:00 | Winner: Budapesti Vasas | ||||
| 1st(1st leg) | Hrvatski Dragovoljac | - | Newry Town FC | 1:0 (0:0) | ||
| 2nd (2nd leg) | Newry Town FC | - | Hrvatski Dragovoljac | 2:0 (1:0) | ||
| 1st(1st leg): 19/06/1999 17:00 | 2nd (2nd leg): 26/06/1999 15:00 | Winner: Newry Town FC | ||||
| 1st(1st leg) | Cementarnica Skopje | - | Kolkheti-1913 Poti | 4:2 (3:2) | ||
| 2nd (2nd leg) | Kolkheti-1913 Poti | - | Cementarnica Skopje | 0:4 (0:3) | ||
| 1st(1st leg): 19/06/1999 17:00 | 2nd (2nd leg): 26/06/1999 15:00 | Winner: Cementarnica Skopje | ||||
| 1st(1st leg) | NK Jedinstvo | - | GÍ Gøta | 3:0 (0:0) | ||
| 2nd (2nd leg) | GÍ Gøta | - | NK Jedinstvo | 1:0 (0:0) | ||
| 1st(1st leg): 19/06/1999 17:00 | 2nd (2nd leg): 26/06/1999 19:00 | Winner: NK Jedinstvo | ||||
| 1st(1st leg) | Maccabi Haifa | - | Qarabağ FK | 1:2 (0:1) | ||
| 2nd (2nd leg) | Qarabağ FK | - | Maccabi Haifa | 0:1 (0:1) | ||
| 1st(1st leg): 19/06/1999 17:00 | 2nd (2nd leg): 26/06/1999 15:00 | Winner: Qarabağ FK | ||||
| 1st(1st leg) | Rudar Velenje | - | Halmstads BK | 0:0 (0:0) | ||
| 2nd (2nd leg) | Halmstads BK | - | Rudar Velenje | 2:2 (2:1) | ||
| 1st(1st leg): 19/06/1999 19:00 | 2nd (2nd leg): 27/06/1999 16:00 | Winner: Rudar Velenje | ||||
| 1st(1st leg) | Jokerit Helsinki | - | JK Narva Trans | 3:0 (3:0) | ||
| 2nd (2nd leg) | JK Narva Trans | - | Jokerit Helsinki | 1:4 (0:3) | ||
| 1st(1st leg): 20/06/1999 13:30 | 2nd (2nd leg): 26/06/1999 14:00 | Winner: Jokerit Helsinki | ||||
| 1st(1st leg) | Shelbourne FC | - | Neuchâtel Xamax FC | 0:0 (0:0) | ||
| 2nd (2nd leg) | Neuchâtel Xamax FC | - | Shelbourne FC | 2:0 (0:0) | ||
| 1st(1st leg): 20/06/1999 15:00 | 2nd (2nd leg): 27/06/1999 17:00 | Winner: Neuchâtel Xamax FC | ||||
| 1st(1st leg) | Aberystwyth Town | - | Floriana FC | 2:2 (1:1) | ||
| 2nd (2nd leg) | Floriana FC | - | Aberystwyth Town | 2:1 (2:1) | ||
| 1st(1st leg): 20/06/1999 15:30 | 2nd (2nd leg): 26/06/1999 16:00 | Winner: Floriana FC | ||||
| 1st(1st leg) | NK Korotan | - | FC Basel | 0:0 (0:0) | ||
| 2nd (2nd leg) | FC Basel | - | NK Korotan | 6:0 (4:0) | ||
| 1st(1st leg): 20/06/1999 16:00 | 2nd (2nd leg): 26/06/1999 16:30 | Winner: FC Basel | ||||
| 1st(1st leg) | SK Hradec Králové | - | FK Gomel | 1:0 (0:0) | ||
| 2nd (2nd leg) | FK Gomel | - | SK Hradec Králové | 3:1 (1:0, 1:0, 1:0) pso | ||
| 1st(1st leg): 20/06/1999 16:00 | 2nd (2nd leg): 27/06/1999 16:00 | Winner: FK Gomel | ||||
| 1st(1st leg) | Ceahlăul Piatra Neamt | - | FK Ekranas | 1:0 (0:0) | ||
| 2nd (2nd leg) | FK Ekranas | - | Ceahlăul Piatra Neamt | 0:1 (0:1) | ||
| 1st(1st leg): 20/06/1999 16:00 | 2nd (2nd leg): 27/06/1999 16:30 | Winner: Ceahlăul Piatra Neamt | ||||
| 1st(1st leg) | FK Pobeda | - | Ozeta Dukla Trencin | 3:1 (2:1) | ||
| 2nd (2nd leg) | Ozeta Dukla Trencin | - | FK Pobeda | 3:4 (2:0, 3:1, 3:1) pso | ||
| 1st(1st leg): 20/06/1999 16:30 | 2nd (2nd leg): 26/06/1999 16:30 | Winner: FK Pobeda | ||||
