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| 1st(1st leg) | Zrinjski Mostar | - | Legia Warszawa | 1:1 (0:0) | ||
| 2nd (2nd leg) | Legia Warszawa | - | Zrinjski Mostar | 2:0 (1:0) | ||
| 1st(1st leg): 12/07/2016 17:30 | 2nd (2nd leg): 19/07/2016 19:45 | Winner: Legia Warszawa | ||||
| 1st(1st leg) | Qarabağ FK | - | F91 Dudelange | 2:0 (2:0) | ||
| 2nd (2nd leg) | F91 Dudelange | - | Qarabağ FK | 1:1 (0:0) | ||
| 1st(1st leg): 12/07/2016 18:00 | 2nd (2nd leg): 20/07/2016 17:00 | Winner: Qarabağ FK | ||||
| 1st(1st leg) | Dinamo Tbilisi | - | FC Alashkert | 2:0 (0:0) | ||
| 2nd (2nd leg) | FC Alashkert | - | Dinamo Tbilisi | 1:1 (0:1) | ||
| 1st(1st leg): 12/07/2016 18:00 | 2nd (2nd leg): 19/07/2016 16:00 | Winner: Dinamo Tbilisi | ||||
| 1st(1st leg) | Hapoel Be'er Sheva | - | FC Sheriff | 3:2 (1:1) | ||
| 2nd (2nd leg) | FC Sheriff | - | Hapoel Be'er Sheva | 0:0 (0:0) | ||
| 1st(1st leg): 12/07/2016 18:50 | 2nd (2nd leg): 19/07/2016 18:00 | Winner: Hapoel Be'er Sheva | ||||
| 1st(1st leg) | The New Saints | - | APOEL Nikosia | 0:0 (0:0) | ||
| 2nd (2nd leg) | APOEL Nikosia | - | The New Saints | 3:0 (0:0) | ||
| 1st(1st leg): 12/07/2016 19:00 | 2nd (2nd leg): 19/07/2016 18:00 | Winner: APOEL Nikosia | ||||
| 1st(1st leg) | BATE Borisov | - | SJK Seinäjoki | 2:0 (1:0) | ||
| 2nd (2nd leg) | SJK Seinäjoki | - | BATE Borisov | 2:2 (1:2) | ||
| 1st(1st leg): 12/07/2016 19:00 | 2nd (2nd leg): 19/07/2016 18:00 | Winner: BATE Borisov | ||||
| 1st(1st leg) | Valletta FC | - | Crvena Zvezda | 1:2 (1:0) | ||
| 2nd (2nd leg) | Crvena Zvezda | - | Valletta FC | 2:1 (1:1) | ||
| 1st(1st leg): 12/07/2016 19:00 | 2nd (2nd leg): 19/07/2016 19:30 | Winner: Crvena Zvezda | ||||
| 1st(1st leg) | Lincoln Red Imps | - | Celtic FC | 1:0 (0:0) | ||
| 2nd (2nd leg) | Celtic FC | - | Lincoln Red Imps | 3:0 (3:0) | ||
| 1st(1st leg): 12/07/2016 19:00 | 2nd (2nd leg): 20/07/2016 19:45 | Winner: Celtic FC | ||||
| 1st(1st leg) | RB Salzburg | - | FK Liepāja | 1:0 (0:0) | ||
| 2nd (2nd leg) | FK Liepāja | - | RB Salzburg | 0:2 (0:1) | ||
| 1st(1st leg): 12/07/2016 19:30 | 2nd (2nd leg): 19/07/2016 17:00 | Winner: RB Salzburg | ||||
| 1st(1st leg) | Vardar Skopje | - | Dinamo Zagreb | 1:2 (0:2) | ||
| 2nd (2nd leg) | Dinamo Zagreb | - | Vardar Skopje | 3:2 (0:1) | ||
| 1st(1st leg): 12/07/2016 19:45 | 2nd (2nd leg): 20/07/2016 19:45 | Winner: Dinamo Zagreb | ||||
| 1st(1st leg) | FK Žalgiris | - | FK Astana | 0:0 (0:0) | ||
| 2nd (2nd leg) | FK Astana | - | FK Žalgiris | 2:1 (1:0) | ||
| 1st(1st leg): 13/07/2016 18:15 | 2nd (2nd leg): 20/07/2016 15:00 | Winner: FK Astana | ||||
| 1st(1st leg) | Rosenborg BK | - | IFK Norrköping | 3:1 (0:0) | ||
| 2nd (2nd leg) | IFK Norrköping | - | Rosenborg BK | 3:2 (0:1) | ||
| 1st(1st leg): 13/07/2016 18:15 | 2nd (2nd leg): 20/07/2016 18:15 | Winner: Rosenborg BK | ||||
| 1st(1st leg) | PFC Ludogorets Razgrad | - | Mladost Podgorica | 2:0 (2:0) | ||
| 2nd (2nd leg) | Mladost Podgorica | - | PFC Ludogorets Razgrad | 0:3 (0:1) | ||
| 1st(1st leg): 13/07/2016 18:30 | 2nd (2nd leg): 19/07/2016 19:45 | Winner: PFC Ludogorets Razgrad | ||||
| 1st(1st leg) | FK Partizani | - | Ferencvárosi TC | 1:1 (0:0) | ||
| 2nd (2nd leg) | Ferencvárosi TC | - | FK Partizani | 1:3 (1:1, 1:1, 1:1) pso | ||
| 1st(1st leg): 13/07/2016 19:00 | 2nd (2nd leg): 20/07/2016 18:30 | Winner: FK Partizani | ||||
| 1st(1st leg) | Crusaders FC | - | FC København | 0:3 (0:2) | ||
| 2nd (2nd leg) | FC København | - | Crusaders FC | 6:0 (2:0) | ||
| 1st(1st leg): 13/07/2016 19:00 | 2nd (2nd leg): 19/07/2016 18:15 | Winner: FC København | ||||
| 1st(1st leg) | Olimpija Ljubljana | - | AS Trenčín | 3:4 (2:4) | ||
| 2nd (2nd leg) | AS Trenčín | - | Olimpija Ljubljana | 2:3 (2:2) | ||
| 1st(1st leg): 13/07/2016 19:30 | 2nd (2nd leg): 20/07/2016 19:15 | Winner: AS Trenčín | ||||
| 1st(1st leg) | Dundalk FC | - | FH Hafnarfjörður | 1:1 (0:0) | ||
| 2nd (2nd leg) | FH Hafnarfjörður | - | Dundalk FC | 2:2 (1:0) | ||
| 1st(1st leg): 13/07/2016 19:45 | 2nd (2nd leg): 20/07/2016 20:15 | Winner: Dundalk FC | ||||
