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| U | Sliema Wanderers | - | Maccabi Netanya | 0:0 (0:0) | ||
| R | Maccabi Netanya | - | Sliema Wanderers | 3:0 (0:0) | ||
| U: 14.07.2009 17:45 | R: 23.07.2009 19:00 | Winnaars: Maccabi Netanya | ||||
| U | Crusaders FC | - | FK Rabotnički | 1:1 (0:0) | ||
| R | FK Rabotnički | - | Crusaders FC | 4:2 (2:0) | ||
| U: 14.07.2009 20:45 | R: 23.07.2009 17:00 | Winnaars: FK Rabotnički | ||||
| U | FC Zestafoni | - | Helsingborgs IF | 1:2 (0:0) | ||
| R | Helsingborgs IF | - | FC Zestafoni | 2:2 (0:2, 1:2) n.v. | ||
| U: 16.07.2009 16:00 | R: 23.07.2009 20:45 | Winnaars: Helsingborgs IF | ||||
| U | Naftan Novopolotsk | - | KAA Gent | 2:1 (1:0) | ||
| R | KAA Gent | - | Naftan Novopolotsk | 1:0 (0:0) | ||
| U: 16.07.2009 17:00 | R: 23.07.2009 20:00 | Winnaars: KAA Gent | ||||
| U | Milano Kumanovo | - | Slaven Belupo | 0:4 (0:4) | ||
| R | Slaven Belupo | - | Milano Kumanovo | 8:2 (2:0) | ||
| U: 16.07.2009 17:00 | R: 23.07.2009 19:00 | Winnaars: Slaven Belupo | ||||
| U | MŠK Žilina | - | Dacia Chişinău | 2:0 (0:0) | ||
| R | Dacia Chişinău | - | MŠK Žilina | 0:1 (0:0) | ||
| U: 16.07.2009 17:30 | R: 23.07.2009 18:30 | Winnaars: MŠK Žilina | ||||
| U | Flamurtari Vlorë | - | Motherwell FC | 1:0 (0:0) | ||
| R | Motherwell FC | - | Flamurtari Vlorë | 8:1 (6:0) | ||
| U: 16.07.2009 17:30 | R: 23.07.2009 20:45 | Winnaars: Motherwell FC | ||||
| U | FC Honka | - | Bangor City | 2:0 (1:0) | ||
| R | Bangor City | - | FC Honka | 0:1 (0:1) | ||
| U: 16.07.2009 18:00 | R: 23.07.2009 21:05 | Winnaars: FC Honka | ||||
| U | FK Liepājas Metalurgs | - | Dinamo Tbilisi | 2:1 (1:0) | ||
| R | Dinamo Tbilisi | - | FK Liepājas Metalurgs | 3:1 (1:0) | ||
| U: 16.07.2009 18:00 | R: 23.07.2009 16:00 | Winnaars: Dinamo Tbilisi | ||||
| U | Dinamo Minsk | - | Tromsø IL | 0:0 (0:0) | ||
| R | Tromsø IL | - | Dinamo Minsk | 4:1 (1:0) | ||
| U: 16.07.2009 18:00 | R: 23.07.2009 19:00 | Winnaars: Tromsø IL | ||||
| U | Sloboda Užice | - | FBK Kaunas | 0:0 (0:0) | ||
| R | FBK Kaunas | - | Sloboda Užice | 1:1 (0:0) | ||
| U: 16.07.2009 18:00 | R: 23.07.2009 18:00 | Winnaars: Sloboda Užice | ||||
| U | FC Zimbru | - | Paços de Ferreira | 0:0 (0:0) | ||
| R | Paços de Ferreira | - | FC Zimbru | 1:0 (0:0) | ||
| U: 16.07.2009 18:30 | R: 23.07.2009 22:00 | Winnaars: Paços de Ferreira | ||||
| U | Metalurh Donetsk | - | MTZ-Ripo | 3:0 (2:0) | ||
| R | MTZ-Ripo | - | Metalurh Donetsk | 1:2 (1:1) | ||
| U: 16.07.2009 18:30 | R: 23.07.2009 17:00 | Winnaars: Metalurh Donetsk | ||||
| U | Tobyl Kostanay | - | Galatasaray | 1:1 (1:0) | ||
| R | Galatasaray | - | Tobyl Kostanay | 2:0 (0:0) | ||
| U: 16.07.2009 18:30 | R: 23.07.2009 20:00 | Winnaars: Galatasaray | ||||
| U | Skonto FC | - | Derry City | 1:1 (1:1) | ||
| R | Derry City | - | Skonto FC | 1:0 (0:0) | ||
| U: 16.07.2009 18:45 | R: 23.07.2009 20:00 | Winnaars: Derry City | ||||
| U | Rosenborg BK | - | Qarabağ FK | 0:0 (0:0) | ||
| R | Qarabağ FK | - | Rosenborg BK | 1:0 (1:0) | ||
| U: 16.07.2009 19:00 | R: 23.07.2009 17:00 | Winnaars: Qarabağ FK | ||||
| U | Anorthosis Famagusta | - | OFK Petrovac | 2:1 (2:0) | ||
| R | OFK Petrovac | - | Anorthosis Famagusta | 3:1 (1:1, 2:1) n.v. | ||
| U: 16.07.2009 19:00 | R: 23.07.2009 17:00 | Winnaars: OFK Petrovac | ||||
| U | Sigma Olomouc | - | Fram Reykjavík | 1:1 (0:1) | ||
| R | Fram Reykjavík | - | Sigma Olomouc | 0:2 (0:0) | ||
| U: 16.07.2009 19:00 | R: 23.07.2009 21:00 | Winnaars: Sigma Olomouc | ||||
| U | IF Elfsborg | - | Szombathelyi Haladás | 3:0 (0:0) | ||
| R | Szombathelyi Haladás | - | IF Elfsborg | 0:0 (0:0) | ||
| U: 16.07.2009 19:00 | R: 23.07.2009 19:00 | Winnaars: IF Elfsborg | ||||
| U | FK Sūduva | - | Randers FC | 0:1 (0:1) | ||
| R | Randers FC | - | FK Sūduva | 1:1 (1:0) | ||
| U: 16.07.2009 19:00 | R: 23.07.2009 19:00 | Winnaars: Randers FC | ||||
| U | FK Vetra | - | HJK Helsinki | 0:1 (0:1) | ||
| R | HJK Helsinki | - | FK Vetra | 1:3 (1:2) | ||
| U: 16.07.2009 19:00 | R: 23.07.2009 18:00 | Winnaars: FK Vetra | ||||
| U | Bnei Yehuda Tel Aviv | - | FC Dinaburg | 4:0 (2:0) | ||
| R | FC Dinaburg | - | Bnei Yehuda Tel Aviv | 0:1 (0:1) | ||
| U: 16.07.2009 19:00 | R: 23.07.2009 18:00 | Winnaars: Bnei Yehuda Tel Aviv | ||||
| U | Cherno More Varna | - | FC Iskra-Stal | 1:0 (1:0) | ||
| R | FC Iskra-Stal | - | Cherno More Varna | 0:3 (0:1) | ||
| U: 16.07.2009 19:00 | R: 23.07.2009 19:00 | Winnaars: Cherno More Varna | ||||
| U | Sturm Graz | - | Široki Brijeg | 2:1 (2:0) | ||
| R | Široki Brijeg | - | Sturm Graz | 1:1 (0:1) | ||
| U: 16.07.2009 19:15 | R: 23.07.2009 20:15 | Winnaars: Sturm Graz | ||||
| U | Rapid Wien | - | FK Vllaznia | 5:0 (1:0) | ||
| R | FK Vllaznia | - | Rapid Wien | 0:3 (0:0) | ||
| U: 16.07.2009 19:15 | R: 23.07.2009 20:15 | Winnaars: Rapid Wien | ||||
| U | FC Basel 1893 | - | FC Santa Coloma | 3:0 (1:0) | ||
| R | FC Santa Coloma | - | FC Basel 1893 | 1:4 (1:3) | ||
| U: 16.07.2009 19:30 | R: 23.07.2009 19:00 | Winnaars: FC Basel 1893 | ||||
| U | Omonia Nikosia | - | HB Tórshavn | 4:0 (3:0) | ||
| R | HB Tórshavn | - | Omonia Nikosia | 1:4 (0:1) | ||
| U: 16.07.2009 19:30 | R: 23.07.2009 20:00 | Winnaars: Omonia Nikosia | ||||
| U | Aalborg BK | - | Slavija Sarajevo | 0:0 (0:0) | ||
| R | Slavija Sarajevo | - | Aalborg BK | 3:1 (1:0) | ||
| U: 16.07.2009 19:30 | R: 23.07.2009 20:15 | Winnaars: Slavija Sarajevo | ||||
| U | FCSB | - | Újpest FC | 2:0 (0:0) | ||
| R | Újpest FC | - | FCSB | 1:2 (0:0) | ||
| U: 16.07.2009 19:30 | R: 23.07.2009 19:45 | Winnaars: FCSB | ||||
| U | ND Gorica | - | FC Lahti | 1:0 (1:0) | ||
| R | FC Lahti | - | ND Gorica | 2:0 (0:0) | ||
| U: 16.07.2009 20:00 | R: 23.07.2009 17:30 | Winnaars: FC Lahti | ||||
| U | Legia Warschau | - | FC Olimpi Rustavi | 3:0 (1:0) | ||
| R | FC Olimpi Rustavi | - | Legia Warschau | 0:1 (0:1) | ||
| U: 16.07.2009 20:00 | R: 23.07.2009 15:30 | Winnaars: Legia Warschau | ||||
| U | FC Differdange 03 | - | HNK Rijeka | 1:0 (0:0) | ||
| R | HNK Rijeka | - | FC Differdange 03 | 3:0 (2:0) | ||
| U: 16.07.2009 20:00 | R: 23.07.2009 21:05 | Winnaars: HNK Rijeka | ||||
| U | Rudar Velenje | - | Rode Ster Belgrado | 0:1 (0:0) | ||
| R | Rode Ster Belgrado | - | Rudar Velenje | 4:0 (1:0) | ||
| U: 16.07.2009 20:00 | R: 23.07.2009 20:30 | Winnaars: Rode Ster Belgrado | ||||
| U | Brøndby IF | - | FC Flora | 0:1 (0:0) | ||
| R | FC Flora | - | Brøndby IF | 1:4 (0:3) | ||
| U: 16.07.2009 20:05 | R: 23.07.2009 17:45 | Winnaars: Brøndby IF | ||||
| U | FK Sarajevo | - | Spartak Trnava | 1:0 (1:0) | ||
| R | Spartak Trnava | - | FK Sarajevo | 1:1 (1:0) | ||
| U: 16.07.2009 20:15 | R: 23.07.2009 19:30 | Winnaars: FK Sarajevo | ||||
| U | AC Juvenes/Dogana | - | Polonia Warszawa | 0:1 (0:1) | ||
| R | Polonia Warszawa | - | AC Juvenes/Dogana | 4:0 (2:0) | ||
| U: 16.07.2009 20:30 | R: 23.07.2009 18:00 | Winnaars: Polonia Warszawa | ||||
| U | Falkirk FC | - | FC Vaduz | 1:0 (0:0) | ||
| R | FC Vaduz | - | Falkirk FC | 2:0 (1:0, 1:0) n.v. | ||
| U: 16.07.2009 20:30 | R: 23.07.2009 19:30 | Winnaars: FC Vaduz | ||||
| U | St Patrick's Athletic | - | Valletta FC | 1:1 (1:0) | ||
| R | Valletta FC | - | St Patrick's Athletic | 0:1 (0:0) | ||
| U: 16.07.2009 20:45 | R: 23.07.2009 17:30 | Winnaars: St Patrick's Athletic | ||||
| U | NAC Breda | - | Gandzasar Kapan | 6:0 (1:0) | ||
| R | Gandzasar Kapan | - | NAC Breda | 0:2 (0:2) | ||
| U: 16.07.2009 20:45 | R: 23.07.2009 17:30 | Winnaars: NAC Breda | ||||
| U | KR Reykjavík | - | AE Lárissa | 2:0 (0:0) | ||
| R | AE Lárissa | - | KR Reykjavík | 1:1 (1:0) | ||
| U: 16.07.2009 21:15 | R: 23.07.2009 19:00 | Winnaars: KR Reykjavík | ||||
