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| H | Bnei Yehuda Tel Aviv | - | Paços de Ferreira | 1:0 (0:0) | ||
| R | Paços de Ferreira | - | Bnei Yehuda Tel Aviv | 0:1 (0:1) | ||
| H: 28.07.2009 18:00 | R: 06.08.2009 22:00 | Sieger: Bnei Yehuda Tel Aviv | ||||
| H | Dinamo Tbilisi | - | Crvena Zvezda | 2:0 (1:0) | ||
| R | Crvena Zvezda | - | Dinamo Tbilisi | 5:2 (3:2) | ||
| H: 30.07.2009 16:00 | R: 06.08.2009 20:45 | Sieger: Crvena Zvezda | ||||
| H | FK Rabotnički | - | Odense BK | 3:4 (2:2) | ||
| R | Odense BK | - | FK Rabotnički | 3:0 (0:0) | ||
| H: 30.07.2009 17:00 | R: 06.08.2009 20:05 | Sieger: Odense BK | ||||
| H | OFK Petrovac | - | Sturm Graz | 1:2 (1:0) | ||
| R | Sturm Graz | - | OFK Petrovac | 5:0 (2:0) | ||
| H: 30.07.2009 17:00 | R: 06.08.2009 19:15 | Sieger: Sturm Graz | ||||
| H | FC Honka | - | Qarabağ FK | 0:1 (0:0) | ||
| R | Qarabağ FK | - | FC Honka | 2:1 (1:1) | ||
| H: 30.07.2009 17:30 | R: 06.08.2009 17:00 | Sieger: Qarabağ FK | ||||
| H | Maccabi Netanya | - | Galatasaray | 1:4 (1:1) | ||
| R | Galatasaray | - | Maccabi Netanya | 6:0 (2:0) | ||
| H: 30.07.2009 18:40 | R: 06.08.2009 20:00 | Sieger: Galatasaray | ||||
| H | Fredrikstad FK | - | Lech Poznań | 1:6 (0:3) | ||
| R | Lech Poznań | - | Fredrikstad FK | 1:2 (0:2) | ||
| H: 30.07.2009 19:00 | R: 06.08.2009 18:30 | Sieger: Lech Poznań | ||||
| H | IFK Göteborg | - | Hapoel Tel Aviv | 1:3 (1:0) | ||
| R | Hapoel Tel Aviv | - | IFK Göteborg | 1:1 (1:0) | ||
| H: 30.07.2009 19:00 | R: 06.08.2009 19:00 | Sieger: Hapoel Tel Aviv | ||||
| H | Metalurh Donetsk | - | Interblock Ljubljana | 2:0 (1:0) | ||
| R | Interblock Ljubljana | - | Metalurh Donetsk | 0:3 (0:0) | ||
| H: 30.07.2009 19:00 | R: 06.08.2009 20:00 | Sieger: Metalurh Donetsk | ||||
| H | Vålerenga IF | - | PAOK Saloniki | 1:2 (1:2) | ||
| R | PAOK Saloniki | - | Vålerenga IF | 0:1 (0:0) | ||
| H: 30.07.2009 19:00 | R: 06.08.2009 20:45 | Sieger: PAOK Saloniki | ||||
| H | Tromsø IL | - | Slaven Belupo | 2:1 (0:1) | ||
| R | Slaven Belupo | - | Tromsø IL | 0:2 (0:1) | ||
| H: 30.07.2009 19:00 | R: 06.08.2009 19:00 | Sieger: Tromsø IL | ||||
| H | Brøndby IF | - | Legia Warszawa | 1:1 (0:1) | ||
| R | Legia Warszawa | - | Brøndby IF | 2:2 (1:1) | ||
| H: 30.07.2009 19:00 | R: 06.08.2009 20:00 | Sieger: Brøndby IF | ||||
| H | CSKA Sofia | - | Derry City | 1:0 (0:0) | ||
| R | Derry City | - | CSKA Sofia | 1:1 (0:0) | ||
| H: 30.07.2009 19:00 | R: 06.08.2009 20:00 | Sieger: CSKA Sofia | ||||
| H | FK Vetra | - | Fulham FC | 0:3 (0:1) | ||
| R | Fulham FC | - | FK Vetra | 3:0 (0:0) | ||
| H: 30.07.2009 19:00 | R: 06.08.2009 21:00 | Sieger: Fulham FC | ||||
| H | Rapid Wien | - | APOP Kinyras | 2:1 (1:0) | ||
| R | APOP Kinyras | - | Rapid Wien | 2:2 (1:1, 2:1) n.V. | ||
| H: 30.07.2009 19:15 | R: 06.08.2009 19:15 | Sieger: Rapid Wien | ||||
| H | Vojvodina | - | Austria Wien | 1:1 (1:1) | ||
| R | Austria Wien | - | Vojvodina | 4:2 (1:1) | ||
| H: 30.07.2009 19:15 | R: 06.08.2009 19:15 | Sieger: Austria Wien | ||||
| H | FC Vaduz | - | Slovan Liberec | 0:1 (0:1) | ||
| R | Slovan Liberec | - | FC Vaduz | 2:0 (2:0) | ||
| H: 30.07.2009 19:30 | R: 06.08.2009 18:00 | Sieger: Slovan Liberec | ||||
| H | MŠK Žilina | - | Hajduk Split | 1:1 (0:0) | ||
| R | Hajduk Split | - | MŠK Žilina | 0:1 (0:0) | ||
| H: 30.07.2009 19:30 | R: 06.08.2009 21:00 | Sieger: MŠK Žilina | ||||
| H | FC Steaua Bucureşti | - | Motherwell FC | 3:0 (2:0) | ||
| R | Motherwell FC | - | FC Steaua Bucureşti | 1:3 (1:0) | ||
| H: 30.07.2009 19:45 | R: 06.08.2009 20:45 | Sieger: FC Steaua Bucureşti | ||||
| H | FC Vaslui | - | Omonia Nikosia | 2:0 (1:0) | ||
| R | Omonia Nikosia | - | FC Vaslui | 1:1 (0:0) | ||
| H: 30.07.2009 20:00 | R: 04.08.2009 18:00 | Sieger: FC Vaslui | ||||
| H | Polonia Warszawa | - | NAC Breda | 0:1 (0:1) | ||
| R | NAC Breda | - | Polonia Warszawa | 3:1 (2:0) | ||
| H: 30.07.2009 20:00 | R: 06.08.2009 20:00 | Sieger: NAC Breda | ||||
| H | Slavija Sarajevo | - | MFK Košice | 0:2 (0:1) | ||
| R | MFK Košice | - | Slavija Sarajevo | 3:1 (1:1) | ||
| H: 30.07.2009 20:15 | R: 06.08.2009 17:00 | Sieger: MFK Košice | ||||
| H | Randers FC | - | Hamburger SV | 0:4 (0:2) | ||
| R | Hamburger SV | - | Randers FC | 0:1 (0:1) | ||
| H: 30.07.2009 20:30 | R: 06.08.2009 20:30 | Sieger: Hamburger SV | ||||
| H | Club Brugge KV | - | FC Lahti | 3:2 (2:1) | ||
| R | FC Lahti | - | Club Brugge KV | 1:1 (0:0) | ||
| H: 30.07.2009 20:30 | R: 06.08.2009 19:00 | Sieger: Club Brugge KV | ||||
| H | Helsingborgs IF | - | FK Sarajevo | 2:1 (1:1) | ||
| R | FK Sarajevo | - | Helsingborgs IF | 5:4 (1:1, 2:1, 2:1) i.E. | ||
| H: 30.07.2009 20:45 | R: 06.08.2009 20:15 | Sieger: FK Sarajevo | ||||
| H | AS Roma | - | KAA Gent | 3:1 (0:1) | ||
| R | KAA Gent | - | AS Roma | 1:7 (0:1) | ||
| H: 30.07.2009 20:45 | R: 06.08.2009 20:30 | Sieger: AS Roma | ||||
| H | PSV Eindhoven | - | Cherno More Varna | 1:0 (0:0) | ||
| R | Cherno More Varna | - | PSV Eindhoven | 0:1 (0:1) | ||
| H: 30.07.2009 20:45 | R: 06.08.2009 18:00 | Sieger: PSV Eindhoven | ||||
| H | St Patrick's Athletic | - | Krylia Sovetov | 1:0 (0:0) | ||
| R | Krylia Sovetov | - | St Patrick's Athletic | 3:2 (1:0) | ||
| H: 30.07.2009 20:45 | R: 06.08.2009 16:00 | Sieger: St Patrick's Athletic | ||||
| H | Aberdeen FC | - | Sigma Olomouc | 1:5 (1:1) | ||
| R | Sigma Olomouc | - | Aberdeen FC | 3:0 (3:0) | ||
| H: 30.07.2009 20:45 | R: 06.08.2009 20:00 | Sieger: Sigma Olomouc | ||||
| H | FK Sloboda Užice | - | Lille OSC | 0:2 (0:2) | ||
| R | Lille OSC | - | FK Sloboda Užice | 2:0 (0:0) | ||
| H: 30.07.2009 20:45 | R: 06.08.2009 19:00 | Sieger: Lille OSC | ||||
| H | Fenerbahçe | - | Budapest Honvéd | 5:1 (3:0) | ||
| R | Budapest Honvéd | - | Fenerbahçe | 1:1 (0:1) | ||
| H: 30.07.2009 20:45 | R: 06.08.2009 20:00 | Sieger: Fenerbahçe | ||||
| H | HNK Rijeka | - | Metalist Kharkiv | 1:2 (0:1) | ||
| R | Metalist Kharkiv | - | HNK Rijeka | 2:0 (1:0) | ||
| H: 30.07.2009 21:00 | R: 06.08.2009 20:00 | Sieger: Metalist Kharkiv | ||||
| H | KR Reykjavík | - | FC Basel | 2:2 (2:0) | ||
| R | FC Basel | - | KR Reykjavík | 3:1 (1:1) | ||
| H: 30.07.2009 21:15 | R: 06.08.2009 19:30 | Sieger: FC Basel | ||||
| H | Athletic Bilbao | - | BSC Young Boys | 0:1 (0:1) | ||
| R | BSC Young Boys | - | Athletic Bilbao | 1:2 (0:1) | ||
| H: 30.07.2009 21:30 | R: 06.08.2009 19:30 | Sieger: Athletic Bilbao | ||||
| H | Sporting Braga | - | IF Elfsborg | 1:2 (0:1) | ||
| R | IF Elfsborg | - | Sporting Braga | 2:0 (2:0) | ||
| H: 30.07.2009 21:45 | R: 06.08.2009 20:00 | Sieger: IF Elfsborg | ||||
