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| U | Herfølge BK | - | MŠK Žilina | 0:2 (0:0) | ||
| R | MŠK Žilina | - | Herfølge BK | 2:0 (1:0) | ||
| U: 19.06.1999 15:00 | R: 26.06.1999 17:30 | Winnaars: MŠK Žilina | ||||
| U | Vålerenga IF | - | FK Ventspils | 1:0 (0:0) | ||
| R | FK Ventspils | - | Vålerenga IF | 2:0 (1:0) | ||
| U: 19.06.1999 16:00 | R: 26.06.1999 17:00 | Winnaars: FK Ventspils | ||||
| U | Polonia Warszawa | - | Tiligul Tiraspol | 4:0 (0:0) | ||
| R | Tiligul Tiraspol | - | Polonia Warszawa | 0:0 (0:0) | ||
| U: 19.06.1999 17:00 | R: 26.06.1999 17:00 | Winnaars: Polonia Warszawa | ||||
| U | Spartak Varna | - | Sint-Truidense VV | 1:2 (1:0) | ||
| R | Sint-Truidense VV | - | Spartak Varna | 6:0 (4:0) | ||
| U: 19.06.1999 17:00 | R: 26.06.1999 20:00 | Winnaars: Sint-Truidense VV | ||||
| U | FCM Bacău | - | FC Ararat | 0:1 (0:0) | ||
| R | FC Ararat | - | FCM Bacău | 1:0 (0:0) | ||
| U: 19.06.1999 17:00 | R: 26.06.1999 15:00 | Winnaars: FC Ararat | ||||
| U | Lokomotiv-96 Vitebsk | - | NK Varteks | 1:2 (0:1) | ||
| R | NK Varteks | - | Lokomotiv-96 Vitebsk | 2:2 (0:1) | ||
| U: 19.06.1999 17:00 | R: 26.06.1999 20:00 | Winnaars: NK Varteks | ||||
| U | ÍA Akranes | - | KF Teuta Durrës | 5:1 (3:1) | ||
| R | KF Teuta Durrës | - | ÍA Akranes | 2:1 (0:1) | ||
| U: 19.06.1999 18:00 | R: 26.06.1999 18:00 | Winnaars: ÍA Akranes | ||||
| U | Union Luxembourg | - | Budapesti Vasas | 1:3 (0:2) | ||
| R | Budapesti Vasas | - | Union Luxembourg | 4:0 (1:0) | ||
| U: 19.06.1999 18:00 | R: 26.06.1999 19:00 | Winnaars: Budapesti Vasas | ||||
| U | Hrvatski Dragovoljac | - | Newry Town FC | 1:0 (0:0) | ||
| R | Newry Town FC | - | Hrvatski Dragovoljac | 2:0 (1:0) | ||
| U: 19.06.1999 18:00 | R: 26.06.1999 16:00 | Winnaars: Newry Town FC | ||||
| U | Cementarnica Skopje | - | Kolkheti-1913 Poti | 4:2 (3:2) | ||
| R | Kolkheti-1913 Poti | - | Cementarnica Skopje | 0:4 (0:3) | ||
| U: 19.06.1999 18:00 | R: 26.06.1999 16:00 | Winnaars: Cementarnica Skopje | ||||
| U | NK Jedinstvo | - | GÍ Gøta | 3:0 (0:0) | ||
| R | GÍ Gøta | - | NK Jedinstvo | 1:0 (0:0) | ||
| U: 19.06.1999 18:00 | R: 26.06.1999 20:00 | Winnaars: NK Jedinstvo | ||||
| U | Maccabi Haifa | - | Qarabağ FK | 1:2 (0:1) | ||
| R | Qarabağ FK | - | Maccabi Haifa | 0:1 (0:1) | ||
| U: 19.06.1999 18:00 | R: 26.06.1999 16:00 | Winnaars: Qarabağ FK | ||||
| U | Rudar Velenje | - | Halmstads BK | 0:0 (0:0) | ||
| R | Halmstads BK | - | Rudar Velenje | 2:2 (2:1) | ||
| U: 19.06.1999 20:00 | R: 27.06.1999 17:00 | Winnaars: Rudar Velenje | ||||
| U | Jokerit Helsinki | - | JK Narva Trans | 3:0 (3:0) | ||
| R | JK Narva Trans | - | Jokerit Helsinki | 1:4 (0:3) | ||
| U: 20.06.1999 14:30 | R: 26.06.1999 15:00 | Winnaars: Jokerit Helsinki | ||||
| U | Shelbourne FC | - | Neuchâtel Xamax FC | 0:0 (0:0) | ||
| R | Neuchâtel Xamax FC | - | Shelbourne FC | 2:0 (0:0) | ||
| U: 20.06.1999 16:00 | R: 27.06.1999 18:00 | Winnaars: Neuchâtel Xamax FC | ||||
| U | Aberystwyth Town | - | Floriana FC | 2:2 (1:1) | ||
| R | Floriana FC | - | Aberystwyth Town | 2:1 (2:1) | ||
| U: 20.06.1999 16:30 | R: 26.06.1999 17:00 | Winnaars: Floriana FC | ||||
| U | NK Korotan | - | FC Basel | 0:0 (0:0) | ||
| R | FC Basel | - | NK Korotan | 6:0 (4:0) | ||
| U: 20.06.1999 17:00 | R: 26.06.1999 17:30 | Winnaars: FC Basel | ||||
| U | SK Hradec Králové | - | FK Gomel | 1:0 (0:0) | ||
| R | FK Gomel | - | SK Hradec Králové | 3:1 (1:0, 1:0, 1:0) d.p. | ||
| U: 20.06.1999 17:00 | R: 27.06.1999 17:00 | Winnaars: FK Gomel | ||||
| U | Ceahlăul Piatra Neamt | - | FK Ekranas | 1:0 (0:0) | ||
| R | FK Ekranas | - | Ceahlăul Piatra Neamt | 0:1 (0:1) | ||
| U: 20.06.1999 17:00 | R: 27.06.1999 17:30 | Winnaars: Ceahlăul Piatra Neamt | ||||
| U | FK Pobeda | - | Ozeta Dukla Trencin | 3:1 (2:1) | ||
| R | Ozeta Dukla Trencin | - | FK Pobeda | 3:4 (2:0, 3:1, 3:1) d.p. | ||
| U: 20.06.1999 17:30 | R: 26.06.1999 17:30 | Winnaars: FK Pobeda | ||||
