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| U | Ulisses FC | - | FC Sheriff | 0:1 (0:0) | ||
| R | FC Sheriff | - | Ulisses FC | 1:0 (0:0) | ||
| U: 17.07.2012 17:00 | R: 24.07.2012 19:00 | Winnaars: FC Sheriff | ||||
| U | FC Flora | - | FC Basel | 0:2 (0:0) | ||
| R | FC Basel | - | FC Flora | 3:0 (2:0) | ||
| U: 17.07.2012 17:45 | R: 24.07.2012 20:00 | Winnaars: FC Basel | ||||
| U | HJK Helsinki | - | KR Reykjavík | 7:0 (2:0) | ||
| R | KR Reykjavík | - | HJK Helsinki | 1:2 (0:0) | ||
| U: 17.07.2012 18:00 | R: 24.07.2012 21:15 | Winnaars: HJK Helsinki | ||||
| U | Neftçi PFK | - | FC Zestafoni | 3:0 (2:0) | ||
| R | FC Zestafoni | - | Neftçi PFK | 2:2 (2:1) | ||
| U: 17.07.2012 18:00 | R: 24.07.2012 19:00 | Winnaars: Neftçi PFK | ||||
| U | F91 Dudelange | - | RB Salzburg | 1:0 (0:0) | ||
| R | RB Salzburg | - | F91 Dudelange | 4:3 (2:1) | ||
| U: 17.07.2012 18:30 | R: 24.07.2012 18:00 | Winnaars: F91 Dudelange | ||||
| U | Slovan Liberec | - | Shakter Karaganda | 1:0 (1:0) | ||
| R | Shakter Karaganda | - | Slovan Liberec | 1:1 (1:0, 1:0) n.v. | ||
| U: 17.07.2012 19:00 | R: 24.07.2012 15:00 | Winnaars: Slovan Liberec | ||||
| U | MŠK Žilina | - | Ironi Kiryat Shmona | 1:0 (0:0) | ||
| R | Ironi Kiryat Shmona | - | MŠK Žilina | 2:0 (0:0) | ||
| U: 17.07.2012 19:30 | R: 24.07.2012 18:30 | Winnaars: Ironi Kiryat Shmona | ||||
| U | The New Saints | - | Helsingborgs IF | 0:0 (0:0) | ||
| R | Helsingborgs IF | - | The New Saints | 3:0 (2:0) | ||
| U: 17.07.2012 20:15 | R: 25.07.2012 19:15 | Winnaars: Helsingborgs IF | ||||
| U | KF Skënderbeu | - | Debreceni VSC | 1:0 (0:0) | ||
| R | Debreceni VSC | - | KF Skënderbeu | 3:0 (1:0) | ||
| U: 17.07.2012 20:30 | R: 24.07.2012 20:30 | Winnaars: Debreceni VSC | ||||
| U | Valletta FC | - | Partizan | 1:4 (0:3) | ||
| R | Partizan | - | Valletta FC | 3:1 (1:0) | ||
| U: 17.07.2012 20:45 | R: 24.07.2012 20:45 | Winnaars: Partizan | ||||
| U | Shamrock Rovers | - | FK Ekranas | 0:0 (0:0) | ||
| R | FK Ekranas | - | Shamrock Rovers | 2:1 (1:0) | ||
| U: 17.07.2012 21:00 | R: 24.07.2012 19:00 | Winnaars: FK Ekranas | ||||
| U | BATE Borisov | - | Vardar Skopje | 3:2 (1:0) | ||
| R | Vardar Skopje | - | BATE Borisov | 0:0 (0:0) | ||
| U: 18.07.2012 18:00 | R: 25.07.2012 20:00 | Winnaars: BATE Borisov | ||||
| U | AEL Limassol | - | Linfield FC | 3:0 (2:0) | ||
| R | Linfield FC | - | AEL Limassol | 0:0 (0:0) | ||
| U: 18.07.2012 19:00 | R: 25.07.2012 20:45 | Winnaars: AEL Limassol | ||||
| U | NK Maribor | - | Željezničar Sarajevo | 4:1 (0:1) | ||
| R | Željezničar Sarajevo | - | NK Maribor | 1:2 (0:1) | ||
| U: 18.07.2012 20:00 | R: 24.07.2012 21:00 | Winnaars: NK Maribor | ||||
| U | PFC Ludogorets Razgrad | - | Dinamo Zagreb | 1:1 (0:0) | ||
| R | Dinamo Zagreb | - | PFC Ludogorets Razgrad | 3:2 (1:2) | ||
| U: 18.07.2012 20:00 | R: 25.07.2012 20:45 | Winnaars: Dinamo Zagreb | ||||
| U | Molde FK | - | FK Ventspils | 3:0 (0:0) | ||
| R | FK Ventspils | - | Molde FK | 1:1 (1:1) | ||
| U: 18.07.2012 20:45 | R: 24.07.2012 17:30 | Winnaars: Molde FK | ||||
| U | FK Budućnost Podgorica | - | Śląsk Wrocław | 0:2 (0:1) | ||
| R | Śląsk Wrocław | - | FK Budućnost Podgorica | 0:1 (0:1) | ||
| U: 18.07.2012 20:45 | R: 25.07.2012 20:45 | Winnaars: Śląsk Wrocław | ||||
