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| H | Víkingur | - | FK Gomel | 0:6 (0:0) | ||
| R | FK Gomel | - | Víkingur | 4:0 (0:0) | ||
| H: 03.07.2012 17:30 | R: 12.07.2012 18:00 | Sieger: FK Gomel | ||||
| H | KF Shkëndija 79 | - | Portadown FC | 0:0 (0:0) | ||
| R | Portadown FC | - | KF Shkëndija 79 | 2:1 (0:1) | ||
| H: 03.07.2012 17:30 | R: 10.07.2012 20:45 | Sieger: Portadown FC | ||||
| H | Khazar Lankaran | - | JK Nõmme Kalju | 2:2 (2:1) | ||
| R | JK Nõmme Kalju | - | Khazar Lankaran | 0:2 (0:1) | ||
| H: 05.07.2012 17:00 | R: 10.07.2012 17:45 | Sieger: Khazar Lankaran | ||||
| H | JK Narva Trans | - | Inter Baku | 0:5 (0:2) | ||
| R | Inter Baku | - | JK Narva Trans | 2:0 (1:0) | ||
| H: 05.07.2012 17:30 | R: 12.07.2012 18:00 | Sieger: Inter Baku | ||||
| H | FK Renova | - | AC Libertas | 4:0 (2:0) | ||
| R | AC Libertas | - | FK Renova | 0:4 (0:1) | ||
| H: 05.07.2012 17:30 | R: 12.07.2012 20:30 | Sieger: FK Renova | ||||
| H | FK Jagodina | - | FK Ordabasy | 0:1 (0:0) | ||
| R | FK Ordabasy | - | FK Jagodina | 0:0 (0:0) | ||
| H: 05.07.2012 17:30 | R: 12.07.2012 16:00 | Sieger: FK Ordabasy | ||||
| H | Kuopion PS | - | Llanelli AFC | 2:1 (2:1) | ||
| R | Llanelli AFC | - | Kuopion PS | 1:1 (0:0) | ||
| H: 05.07.2012 17:30 | R: 12.07.2012 19:30 | Sieger: Kuopion PS | ||||
| H | FC Levadia | - | FK Šiauliai | 1:0 (0:0) | ||
| R | FK Šiauliai | - | FC Levadia | 2:1 (1:0) | ||
| H: 05.07.2012 17:45 | R: 12.07.2012 18:00 | Sieger: FC Levadia | ||||
| H | FK Baku | - | ND Mura 05 | 0:0 (0:0) | ||
| R | ND Mura 05 | - | FK Baku | 2:0 (1:0) | ||
| H: 05.07.2012 18:00 | R: 12.07.2012 20:00 | Sieger: ND Mura 05 | ||||
| H | IF Elfsborg | - | Floriana FC | 8:0 (5:0) | ||
| R | Floriana FC | - | IF Elfsborg | 0:4 (0:1) | ||
| H: 05.07.2012 18:00 | R: 10.07.2012 17:30 | Sieger: IF Elfsborg | ||||
| H | FK Rudar Pljevlja | - | Shirak FC | 0:1 (0:0) | ||
| R | Shirak FC | - | FK Rudar Pljevlja | 1:1 (1:1) | ||
| H: 05.07.2012 18:00 | R: 12.07.2012 16:00 | Sieger: Shirak FC | ||||
| H | Pyunik FC | - | FK Zeta | 0:3 (0:0) | ||
| R | FK Zeta | - | Pyunik FC | 1:2 (1:1) | ||
| H: 05.07.2012 18:00 | R: 12.07.2012 20:00 | Sieger: FK Zeta | ||||
| H | JJK Jyväskylä | - | Stabæk IF | 2:0 (1:0) | ||
| R | Stabæk IF | - | JJK Jyväskylä | 3:2 (2:1) | ||
| H: 05.07.2012 18:00 | R: 12.07.2012 19:00 | Sieger: JJK Jyväskylä | ||||
| H | FC Differdange 03 | - | NSÍ Runavík | 3:0 (2:0) | ||
| R | NSÍ Runavík | - | FC Differdange 03 | 0:3 (0:2) | ||
| H: 05.07.2012 18:30 | R: 12.07.2012 19:30 | Sieger: FC Differdange 03 | ||||
| H | Dacia Chişinău | - | NK Celje | 1:0 (1:0) | ||
| R | NK Celje | - | Dacia Chişinău | 0:1 (0:1) | ||
| H: 05.07.2012 18:30 | R: 12.07.2012 20:00 | Sieger: Dacia Chişinău | ||||
| H | FK Sūduva | - | FC Daugava | 0:1 (0:0) | ||
| R | FC Daugava | - | FK Sūduva | 2:3 (0:2) | ||
| H: 05.07.2012 18:30 | R: 12.07.2012 18:00 | Sieger: FK Sūduva | ||||
| H | KF Tiranë | - | CS Grevenmacher | 2:0 (2:0) | ||
| R | CS Grevenmacher | - | KF Tiranë | 0:0 (0:0) | ||
| H: 05.07.2012 19:00 | R: 10.07.2012 17:45 | Sieger: KF Tiranë | ||||
| H | Torpedo Kutaisi | - | FK Aktobe | 1:1 (0:0) | ||
| R | FK Aktobe | - | Torpedo Kutaisi | 1:0 (0:0) | ||
| H: 05.07.2012 19:00 | R: 12.07.2012 17:00 | Sieger: FK Aktobe | ||||
| H | Birkirkara FC | - | Metalurg Skopje | 2:2 (0:1) | ||
| R | Metalurg Skopje | - | Birkirkara FC | 0:0 (0:0) | ||
| H: 05.07.2012 19:00 | R: 12.07.2012 17:00 | Sieger: Metalurg Skopje | ||||
| H | FC Santa Coloma | - | NK Osijek | 0:1 (0:0) | ||
| R | NK Osijek | - | FC Santa Coloma | 3:1 (1:0) | ||
| H: 05.07.2012 19:30 | R: 12.07.2012 20:00 | Sieger: NK Osijek | ||||
| H | FK Sarajevo | - | Hibernians FC | 5:2 (2:2) | ||
| R | Hibernians FC | - | FK Sarajevo | 4:4 (4:3) | ||
| H: 05.07.2012 19:30 | R: 12.07.2012 19:30 | Sieger: FK Sarajevo | ||||
| H | FC Twente | - | UE Santa Coloma | 6:0 (2:0) | ||
| R | UE Santa Coloma | - | FC Twente | 0:3 (0:3) | ||
| H: 05.07.2012 19:45 | R: 12.07.2012 19:30 | Sieger: FC Twente | ||||
| H | Lech Poznań | - | Zhetysu Taldykorgan | 2:0 (0:0) | ||
| R | Zhetysu Taldykorgan | - | Lech Poznań | 1:1 (1:1) | ||
| H: 05.07.2012 20:00 | R: 12.07.2012 14:00 | Sieger: Lech Poznań | ||||
| H | Olimpija Ljubljana | - | Jeunesse Esch | 3:0 (0:0) | ||
| R | Jeunesse Esch | - | Olimpija Ljubljana | 0:3 (0:2) | ||
| H: 05.07.2012 20:00 | R: 12.07.2012 18:00 | Sieger: Olimpija Ljubljana | ||||
| H | EB/Streymur | - | Gandzasar Kapan | 3:1 (3:0) | ||
| R | Gandzasar Kapan | - | EB/Streymur | 2:0 (0:0) | ||
| H: 05.07.2012 20:00 | R: 12.07.2012 17:00 | Sieger: Gandzasar Kapan | ||||
| H | MTK Budapest | - | FK Senica | 1:1 (1:0) | ||
| R | FK Senica | - | MTK Budapest | 2:1 (0:0) | ||
| H: 05.07.2012 20:15 | R: 12.07.2012 19:30 | Sieger: FK Senica | ||||
| H | Cefn Druids | - | MyPa-47 | 0:0 (0:0) | ||
| R | MyPa-47 | - | Cefn Druids | 5:0 (3:0) | ||
| H: 05.07.2012 20:30 | R: 12.07.2012 18:30 | Sieger: MyPa-47 | ||||
| H | Flamurtari Vlorë | - | Budapest Honvéd | 0:1 (0:0) | ||
| R | Budapest Honvéd | - | Flamurtari Vlorë | 2:0 (1:0) | ||
| H: 05.07.2012 20:30 | R: 12.07.2012 20:30 | Sieger: Budapest Honvéd | ||||
| H | KF Teuta Durrës | - | Metalurgi Rustavi | 0:3 (0:0) | ||
| R | Metalurgi Rustavi | - | KF Teuta Durrës | 6:1 (3:0) | ||
| H: 05.07.2012 20:30 | R: 12.07.2012 16:00 | Sieger: Metalurgi Rustavi | ||||
| H | SP La Fiorita | - | FK Liepājas Metalurgs | 0:2 (0:1) | ||
| R | FK Liepājas Metalurgs | - | SP La Fiorita | 4:0 (1:0) | ||
| H: 05.07.2012 20:30 | R: 12.07.2012 18:00 | Sieger: FK Liepājas Metalurgs | ||||
| H | Bohemian FC | - | Þór Akureyri | 0:0 (0:0) | ||
| R | Þór Akureyri | - | Bohemian FC | 5:1 (2:1) | ||
| H: 05.07.2012 20:45 | R: 12.07.2012 20:30 | Sieger: Þór Akureyri | ||||
| H | Cliftonville FC | - | Kalmar FF | 1:0 (0:0) | ||
| R | Kalmar FF | - | Cliftonville FC | 4:0 (3:0) | ||
| H: 05.07.2012 20:45 | R: 12.07.2012 19:00 | Sieger: Kalmar FF | ||||
| H | St Patrick's Athletic | - | ÍBV Vestmannaeyjar | 1:0 (1:0) | ||
| R | ÍBV Vestmannaeyjar | - | St Patrick's Athletic | 2:1 (0:0, 1:0) n.V. | ||
| H: 05.07.2012 20:45 | R: 12.07.2012 21:30 | Sieger: St Patrick's Athletic | ||||
| H | Bangor City | - | FC Zimbru | 0:0 (0:0) | ||
| R | FC Zimbru | - | Bangor City | 2:1 (2:1) | ||
| H: 05.07.2012 20:45 | R: 12.07.2012 18:30 | Sieger: FC Zimbru | ||||
| H | Crusaders FC | - | Rosenborg BK | 0:3 (0:1) | ||
| R | Rosenborg BK | - | Crusaders FC | 1:0 (0:0) | ||
| H: 05.07.2012 21:00 | R: 12.07.2012 19:00 | Sieger: Rosenborg BK | ||||
| H | Borac Banja Luka | - | FK Čelik Nikšić | 2:2 (2:1) | ||
| R | FK Čelik Nikšić | - | Borac Banja Luka | 1:1 (0:0) | ||
| H: 05.07.2012 21:05 | R: 12.07.2012 17:30 | Sieger: FK Čelik Nikšić | ||||
| H | FH Hafnarfjörður | - | USV Eschen/Mauren | 2:1 (1:0) | ||
| R | USV Eschen/Mauren | - | FH Hafnarfjörður | 0:1 (0:1) | ||
| H: 05.07.2012 21:15 | R: 12.07.2012 19:30 | Sieger: FH Hafnarfjörður | ||||
