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| U | FK Rabotnički | - | FK Budućnost Podgorica | 1:1 (0:1) | ||
| R | FK Budućnost Podgorica | - | FK Rabotnički | 1:0 (1:0) | ||
| U: 28.06.2016 18:00 | R: 07.07.2016 19:00 | Winnaars: FK Budućnost Podgorica | ||||
| U | FK Partizani | - | Slovan Bratislava | 0:0 (0:0) | ||
| R | Slovan Bratislava | - | FK Partizani | niet gespeeld | ||
| U: 28.06.2016 18:00 | R: 07.07.2016 | |||||
| U | FK Kapaz | - | Dacia Chişinău | 0:0 (0:0) | ||
| R | Dacia Chişinău | - | FK Kapaz | 0:1 (0:0) | ||
| U: 28.06.2016 18:00 | R: 07.07.2016 17:00 | Winnaars: FK Kapaz | ||||
| U | St Patrick's Athletic | - | Jeunesse Esch | 1:0 (1:0) | ||
| R | Jeunesse Esch | - | St Patrick's Athletic | 2:1 (1:0) | ||
| U: 28.06.2016 20:45 | R: 05.07.2016 18:45 | Winnaars: St Patrick's Athletic | ||||
| U | Dila Gori | - | Shirak FC | 1:0 (1:0) | ||
| R | Shirak FC | - | Dila Gori | 4:1 (0:0, 1:0, 1:0) d.p. | ||
| U: 30.06.2016 16:00 | R: 07.07.2016 15:00 | Winnaars: Shirak FC | ||||
| U | FK Aktobe | - | MTK Budapest | 1:1 (1:1) | ||
| R | MTK Budapest | - | FK Aktobe | 2:0 (1:0) | ||
| U: 30.06.2016 16:00 | R: 07.07.2016 18:00 | Winnaars: MTK Budapest | ||||
| U | UE Santa Coloma | - | Lokomotiva Zagreb | 1:3 (0:1) | ||
| R | Lokomotiva Zagreb | - | UE Santa Coloma | 4:1 (2:0) | ||
| U: 30.06.2016 17:00 | R: 07.07.2016 18:00 | Winnaars: Lokomotiva Zagreb | ||||
| U | FK Ventspils | - | Víkingur | 2:0 (2:0) | ||
| R | Víkingur | - | FK Ventspils | 0:2 (0:0) | ||
| U: 30.06.2016 17:00 | R: 07.07.2016 20:00 | Winnaars: FK Ventspils | ||||
| U | FC Admira Wacker | - | Spartak Myjava | 1:1 (1:0) | ||
| R | Spartak Myjava | - | FC Admira Wacker | 2:3 (1:2) | ||
| U: 30.06.2016 17:00 | R: 07.07.2016 17:00 | Winnaars: FC Admira Wacker | ||||
| U | FK Bokelj | - | Vojvodina | 1:1 (1:1) | ||
| R | Vojvodina | - | FK Bokelj | 5:0 (2:0) | ||
| U: 30.06.2016 17:30 | R: 07.07.2016 20:00 | Winnaars: Vojvodina | ||||
| U | FC Levadia | - | HB Tórshavn | 1:1 (0:1) | ||
| R | HB Tórshavn | - | FC Levadia | 0:2 (0:0) | ||
| U: 30.06.2016 18:00 | R: 07.07.2016 19:00 | Winnaars: FC Levadia | ||||
| U | Videoton FC | - | FC Zaria | 3:0 (1:0) | ||
| R | FC Zaria | - | Videoton FC | 2:0 (2:0) | ||
| U: 30.06.2016 18:00 | R: 07.07.2016 19:00 | Winnaars: Videoton FC | ||||
| U | FK Atlantas | - | HJK Helsinki | 0:2 (0:0) | ||
| R | HJK Helsinki | - | FK Atlantas | 1:1 (1:0) | ||
| U: 30.06.2016 18:00 | R: 07.07.2016 18:00 | Winnaars: HJK Helsinki | ||||
| U | Sloboda Tuzla | - | Beitar Jerusalem | 0:0 (0:0) | ||
| R | Beitar Jerusalem | - | Sloboda Tuzla | 1:0 (0:0) | ||
| U: 30.06.2016 18:00 | R: 07.07.2016 18:45 | Winnaars: Beitar Jerusalem | ||||
| U | FK Trakai | - | JK Nõmme Kalju | 2:1 (0:1) | ||
| R | JK Nõmme Kalju | - | FK Trakai | 4:1 (0:1) | ||
| U: 30.06.2016 18:00 | R: 07.07.2016 18:00 | Winnaars: JK Nõmme Kalju | ||||
| U | Balzan FC | - | Neftçi PFK | 0:2 (0:1) | ||
| R | Neftçi PFK | - | Balzan FC | 1:2 (1:0) | ||
| U: 30.06.2016 18:00 | R: 07.07.2016 18:00 | Winnaars: Neftçi PFK | ||||
| U | Dinamo Minsk | - | FK Spartaks | 2:1 (1:0) | ||
| R | FK Spartaks | - | Dinamo Minsk | 0:2 (0:1) | ||
| U: 30.06.2016 18:00 | R: 07.07.2016 18:00 | Winnaars: Dinamo Minsk | ||||
| U | FC Banants | - | Omonia Nikosia | 0:1 (0:1) | ||
| R | Omonia Nikosia | - | FC Banants | 4:1 (0:0, 0:1) n.v. | ||
| U: 30.06.2016 18:00 | R: 07.07.2016 18:30 | Winnaars: Omonia Nikosia | ||||
| U | IFK Göteborg | - | Llandudno FC | 5:0 (3:0) | ||
| R | Llandudno FC | - | IFK Göteborg | 1:2 (0:1) | ||
| U: 30.06.2016 18:30 | R: 07.07.2016 20:00 | Winnaars: IFK Göteborg | ||||
| U | AIK Solna | - | Bala Town | 2:0 (1:0) | ||
| R | Bala Town | - | AIK Solna | 0:2 (0:2) | ||
| U: 30.06.2016 18:30 | R: 07.07.2016 19:30 | Winnaars: AIK Solna | ||||
| U | Europa FC | - | Pyunik FC | 2:0 (2:0) | ||
| R | Pyunik FC | - | Europa FC | 2:1 (1:1) | ||
| U: 30.06.2016 18:30 | R: 07.07.2016 17:00 | Winnaars: Europa FC | ||||
| U | Slavia Sofia | - | Zagłębie Lubin | 1:0 (0:0) | ||
| R | Zagłębie Lubin | - | Slavia Sofia | 3:0 (1:0) | ||
| U: 30.06.2016 18:30 | R: 07.07.2016 18:00 | Winnaars: Zagłębie Lubin | ||||
| U | FC Midtjylland | - | FK Sūduva | 1:0 (0:0) | ||
| R | FK Sūduva | - | FC Midtjylland | 0:1 (0:1) | ||
| U: 30.06.2016 19:00 | R: 07.07.2016 19:00 | Winnaars: FC Midtjylland | ||||
| U | FC Zimbru | - | Chikhura Sachkhere | 0:1 (0:1) | ||
| R | Chikhura Sachkhere | - | FC Zimbru | 2:3 (1:1) | ||
| U: 30.06.2016 19:00 | R: 05.07.2016 18:00 | Winnaars: FC Zimbru | ||||
| U | AEK Larnaca | - | SS Folgore/Falciano | 3:0 (3:0) | ||
| R | SS Folgore/Falciano | - | AEK Larnaca | 1:3 (1:0) | ||
| U: 30.06.2016 19:00 | R: 07.07.2016 20:30 | Winnaars: AEK Larnaca | ||||
| U | FK Kukësi | - | FK Rudar Pljevlja | 1:1 (1:0) | ||
| R | FK Rudar Pljevlja | - | FK Kukësi | 0:1 (0:0) | ||
| U: 30.06.2016 19:00 | R: 07.07.2016 17:30 | Winnaars: FK Kukësi | ||||
| U | FC Vaduz | - | Sileks Kratovo | 3:1 (2:0) | ||
| R | Sileks Kratovo | - | FC Vaduz | 1:2 (1:0) | ||
| U: 30.06.2016 19:00 | R: 07.07.2016 20:00 | Winnaars: FC Vaduz | ||||
| U | FC Differdange 03 | - | Cliftonville FC | 1:1 (1:0) | ||
| R | Cliftonville FC | - | FC Differdange 03 | 2:0 (1:0) | ||
| U: 30.06.2016 19:00 | R: 07.07.2016 20:45 | Winnaars: Cliftonville FC | ||||
| U | Odds BK | - | IFK Mariehamn | 2:0 (0:0) | ||
| R | IFK Mariehamn | - | Odds BK | 1:1 (1:0) | ||
| U: 30.06.2016 19:00 | R: 07.07.2016 18:00 | Winnaars: Odds BK | ||||
| U | Široki Brijeg | - | Birkirkara FC | 1:1 (1:1) | ||
| R | Birkirkara FC | - | Široki Brijeg | 2:0 (1:0) | ||
| U: 30.06.2016 19:00 | R: 05.07.2016 17:45 | Winnaars: Birkirkara FC | ||||
| U | Gabala FK | - | FC Samtredia | 5:1 (3:0) | ||
| R | FC Samtredia | - | Gabala FK | 2:1 (1:1) | ||
| U: 30.06.2016 19:00 | R: 07.07.2016 17:00 | Winnaars: Gabala FK | ||||
| U | Maccabi Tel Aviv | - | ND Gorica | 3:0 (2:0) | ||
| R | ND Gorica | - | Maccabi Tel Aviv | 0:1 (0:1) | ||
| U: 30.06.2016 19:15 | R: 07.07.2016 18:30 | Winnaars: Maccabi Tel Aviv | ||||
| U | PFC Beroe | - | Radnik Bijeljina | 0:0 (0:0) | ||
| R | Radnik Bijeljina | - | PFC Beroe | 0:2 (0:0) | ||
| U: 30.06.2016 19:30 | R: 07.07.2016 18:00 | Winnaars: PFC Beroe | ||||
| U | NK Domžale | - | FC Lusitanos | 3:1 (3:1) | ||
| R | FC Lusitanos | - | NK Domžale | 1:2 (1:2) | ||
| U: 30.06.2016 20:00 | R: 07.07.2016 20:30 | Winnaars: NK Domžale | ||||
| U | NSÍ Runavík | - | Shakhter Soligorsk | 0:2 (0:1) | ||
| R | Shakhter Soligorsk | - | NSÍ Runavík | 5:0 (2:0) | ||
| U: 30.06.2016 20:00 | R: 07.07.2016 20:00 | Winnaars: Shakhter Soligorsk | ||||
| U | KF Teuta Durrës | - | FK Kairat | 0:1 (0:0) | ||
| R | FK Kairat | - | KF Teuta Durrës | 5:0 (2:0) | ||
| U: 30.06.2016 20:00 | R: 07.07.2016 16:45 | Winnaars: FK Kairat | ||||
| U | Connah's Quay Nomads | - | Stabæk IF | 0:0 (0:0) | ||
| R | Stabæk IF | - | Connah's Quay Nomads | 0:1 (0:1) | ||
| U: 30.06.2016 20:15 | R: 07.07.2016 19:00 | Winnaars: Connah's Quay Nomads | ||||
| U | Spartak Trnava | - | Hibernians FC | 3:0 (2:0) | ||
| R | Hibernians FC | - | Spartak Trnava | 0:3 (0:1) | ||
| U: 30.06.2016 20:15 | R: 07.07.2016 20:00 | Winnaars: Spartak Trnava | ||||
| U | SP La Fiorita | - | Debreceni VSC | 0:5 (0:2) | ||
| R | Debreceni VSC | - | SP La Fiorita | 2:0 (1:0) | ||
| U: 30.06.2016 20:30 | R: 07.07.2016 18:00 | Winnaars: Debreceni VSC | ||||
| U | FK Čukarički | - | FK Ordabasy | 3:0 (0:0) | ||
| R | FK Ordabasy | - | FK Čukarički | 3:3 (1:3) | ||
| U: 30.06.2016 20:30 | R: 07.07.2016 14:00 | Winnaars: FK Čukarički | ||||
| U | Aberdeen FC | - | CS FOLA Esch | 3:1 (0:0) | ||
| R | CS FOLA Esch | - | Aberdeen FC | 1:0 (1:0) | ||
| U: 30.06.2016 20:45 | R: 07.07.2016 18:30 | Winnaars: Aberdeen FC | ||||
| U | Linfield FC | - | Cork City | 0:1 (0:0) | ||
| R | Cork City | - | Linfield FC | 1:1 (0:0) | ||
| U: 30.06.2016 20:45 | R: 07.07.2016 20:45 | Winnaars: Cork City | ||||
| U | Shamrock Rovers | - | Rovaniemi PS | 0:2 (0:1) | ||
| R | Rovaniemi PS | - | Shamrock Rovers | 1:1 (1:1) | ||
| U: 30.06.2016 21:00 | R: 07.07.2016 18:00 | Winnaars: Rovaniemi PS | ||||
| U | Heart of Midlothian | - | FC Infonet | 2:1 (2:1) | ||
| R | FC Infonet | - | Heart of Midlothian | 2:4 (0:3) | ||
| U: 30.06.2016 21:00 | R: 06.07.2016 17:45 | Winnaars: Heart of Midlothian | ||||
| U | KF Shkëndija 79 | - | KS Cracovia | 2:0 (1:0) | ||
| R | KS Cracovia | - | KF Shkëndija 79 | 1:2 (0:1) | ||
| U: 30.06.2016 21:00 | R: 07.07.2016 20:00 | Winnaars: KF Shkëndija 79 | ||||
| U | Breiðablik | - | FK Jelgava | 2:3 (1:3) | ||
| R | FK Jelgava | - | Breiðablik | 2:2 (1:2) | ||
| U: 30.06.2016 21:15 | R: 07.07.2016 17:30 | Winnaars: FK Jelgava | ||||
| U | KR Reykjavík | - | Glenavon FC | 2:1 (1:1) | ||
| R | Glenavon FC | - | KR Reykjavík | 0:6 (0:2) | ||
| U: 30.06.2016 21:15 | R: 07.07.2016 20:45 | Winnaars: KR Reykjavík | ||||
| U | Valur Reykjavík | - | Brøndby IF | 1:4 (0:0) | ||
| R | Brøndby IF | - | Valur Reykjavík | 6:0 (3:0) | ||
| U: 30.06.2016 23:00 | R: 07.07.2016 18:30 | Winnaars: Brøndby IF | ||||
