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== Turno preliminare ==
{{TwoLegStart}}
{{TwoLegResult|[[Havnar Bóltfelag]]|FRO|1 - 7|'''[[APOEL FC]]'''|CYP|1 - 1|0 - 6|winner=2}}
{{TwoLegResult|[[Hibernians FC]]|MLT|0 - 4|'''[[Íþróttabandalag Vestmannaeyja|ÍBV Vestmannaeyjar]]'''|ISL|0 - 1|0 - 3|winner=2}}
{{TwoLegResult|[[Glenavon F.C.|Glenavon]]|NIR|1 - 5|'''[[Legia Varsavia]]'''|POL|1 - 1|0 - 4|winner=2}}
{{TwoLegResult|[[Cwmbran Town F.C.|Cwmbran]]|WAL|2 - 12|'''[[FC Național București|Național Bucarest]]'''|ROU|2 - 5|0 - 7|winner=2}}
{{TwoLegResult|[[FK Žalgiris Vilnius]]|LTU|1 - 2|'''[[Hapoel Be'er Sheva]]'''|ISR|0 - 0|1 - 2 <small>([[Tempi supplementari|dts]])</small>|winner=2}}
{{TwoLegResult|[[Zimbru]]|MDA|1 - 4|'''[[Shakhtar Donetsk]]'''|UKR|1 - 1|0 - 3|winner=2}}
{{TwoLegResult|'''[[Dinaburg FC]]'''|LVA|2 - 0|[[Kepez Ganja]]|AZE|1 - 0|1 - 0|winner=1}}
{{TwoLegResult|'''[[Kilmarnock F.C.|Kilmarnock]]'''|SCO|3 - 2|[[Shelbourne F.C.]]|IRL|2 - 1|1 - 1|winner=1}}
{{TwoLegResult|[[HJK Helsinki]]|FIN|1 - 3|'''[[FK Stella Rossa Belgrado|Stella Rossa Belgrado]]'''|SCG|1 - 0|0 - 3|winner=2}}
{{TwoLegResult|[[FK Sloga Jugomagnat]]|MKD|1 - 4|'''[[NK Zagabria]]'''|HRV|1 - 2|0 - 2|winner=2}}
{{TwoLegResult|[[FC Balzers]]|LIE|1 - 5|'''[[BVSC Budapest]]'''|HUN|1 - 3|0 - 2|winner=2}}
{{TwoLegResult|[[Tallinna Sadam]]|EST|2 - 5|'''[[FC Belshina Bobruisk]]'''|BLR|1 - 1|1 - 4|winner=2}}
{{TwoLegResult|'''[[NK Primorje]]'''|SVN|3 - 0|[[Union Luxembourg]]|LUX|2 - 0|1 - 0|winner=1}}
{{TwoLegResult|[[PFC Levski Sofia]]|BGR|2 - 3|'''[[Športový Klub Slovan Bratislava|Slovan Bratislava]]'''|SVK|1 - 1|1 - 2|winner=2}}
{{TwoLegResult|[[Dynamo Batumi]]|GEO|2 - 3|'''[[FC Ararat]]'''|ARM|0 - 3<ref>a tavolino</ref>|2 - 0|winner=2}}
|}
== Sedicesimi di finale ==
{{TwoLegStart}}
{{TwoLegResult|'''[[Kocaelispor]]'''|TUR|3 - 0|[[FC Național București|Național Bucarest]]|ROU|2 - 0|1 - 0|winner=1}}
{{TwoLegResult|[[APOEL FC|APOEL]]|CYP|0 - 4|'''[[Sturm Graz]]'''|AUT|0 - 1|0 - 3|winner=2}}
{{TwoLegResult|[[Íþróttabandalag Vestmannaeyja|ÍBV Vestmannaeyjar]]|ISL|2 - 5|'''[[VfB Stuttgart|Stoccarda]]'''|DEU|1 - 3|1 - 2|winner=2}}
{{TwoLegResult|[[Boavista FC|Boavista]]|PRT|3 - 4|'''[[Shakhtar Donetsk]]'''|UKR|2 - 3|1 - 1|winner=2}}
{{TwoLegResult|'''[[K.F.C. Germinal Beerschot|Germinal Beerschot]]'''|BEL|4 - 3|[[FK Stella Rossa Belgrado|Stella Rossa Belgrado]]|SCG|3 - 2|1 - 1|winner=1}}
{{TwoLegResult|[[Allmänna Idrottsklubben Fotboll|AIK]]|SWE|1 - 2|'''[[NK Primorje]]'''|SVN|0 - 1|1 - 1|winner=2}}
{{TwoLegResult|'''[[AEK Atene]]'''|GRC|9 - 2|[[Dinaburg FC|Dinaburg]]|LVA|5 - 0|4 - 2|winner=1}}
{{TwoLegResult|'''[[Slavia Praga]]'''|CZE|6 - 2|[[FC Lucerna|Lucerna]]|CHE|4 - 2|2 - 0|winner=1}}
{{TwoLegResult|[[Hapoel Be'er Sheva]]|ISR|1 - 14|'''[[Roda JC|Roda Kerkrade]]'''|NLD|1 - 4|0 - 10|winner=2}}
{{TwoLegResult|[[NK Zagabria]]|HRV|5 - 6|'''[[Tromsø I.L.|Tromsø]]'''|NOR|3 - 2|2 - 4|winner=2}}
{{TwoLegResult|'''[[FC København|Copenhagen]]'''|DNK|5 - 0|[[FC Ararat]]|ARM|3 - 0|2 - 0|winner=1}}
{{TwoLegResult|[[FC Belshina Bobruisk]]|BLR|1 - 5|'''[[Lokomotiv Mosca]]'''|RUS|1 - 2|0 - 3|winner=2}}
{{TwoLegResult|'''[[Chelsea F.C.|Chelsea]]'''|ENG|4 - 0|[[Športový Klub Slovan Bratislava|Slovan Bratislava]]|SVK|2 - 0|2 - 0|winner=1}}
{{TwoLegResult|'''[[OGC Nice|Nizza]]'''|FRA|4 - 2|[[Kilmarnock F.C.|Kilmarnock]]|SCO|3 - 1|1 - 1|winner=1}}
{{TwoLegResult|'''[[Real Betis|Betis Siviglia]]'''|ESP|4 - 0|[[BVSC Budapest]]|HUN|2 - 0|2 - 0|winner=1}}
{{TwoLegResult|'''[[Vicenza Calcio|Vicenza]]'''|ITA|3 - 1|[[Legia Varsavia]]|POL|2 - 0|1 - 1|winner=1}}
|}
== Ottavi di finale ==
{{TwoLegStart}}
{{TwoLegResult|[[Tromsø I.L.|Tromsø]]|NOR|4 - 9|'''[[Chelsea F.C.|Chelsea]]'''|ENG|3 - 2|1 - 7|winner=2}}
{{TwoLegResult|[[K.F.C. Germinal Beerschot|Germinal Beerschot]]|BEL|4 - 6|'''[[VfB Stuttgart|Stoccarda]]'''|DEU|0 - 4|4 - 2|winner=2}}
{{TwoLegResult|'''[[Lokomotiv Mosca]]'''|RUS|2 - 1|[[Kocaelispor]]|TUR|2 - 1|0 - 0|winner=1}}
{{TwoLegResult|[[Shakhtar Donetsk]]|UKR|2 - 5|'''[[Vicenza Calcio|Vicenza]]'''|ITA|1 - 3|1 - 2|winner=2}}
{{TwoLegResult|'''[[Real Betis|Betis Siviglia]]'''|ESP|3 - 1|[[FC København|Copenhagen]]|DNK|2 - 0|1 - 1|winner=1}}
{{TwoLegResult|'''[[AEK Atene]]'''|GRC|2 - 1|[[Sturm Graz]]|AUT|2 - 0|0 - 1|winner=1}}
{{TwoLegResult|[[OGC Nice|Nizza]]|FRA|3 - 3|'''[[Slavia Praga]]'''|CZE|2 - 2|1 - 1|winner=2}}
{{TwoLegResult|[[NK Primorje]]|SVN|0 - 6|'''[[Roda JC|Roda Kerkrade]]'''|NLD|0 - 2|0 - 4|winner=2}}
|}
== Quarti di finale ==
{{TwoLegStart}}
{{TwoLegResult|[[Roda JC|Roda Kerkrade]]|NLD|1 - 9|'''[[Vicenza Calcio|Vicenza]]'''|ITA|1 - 4|0 - 5|winner=2}}
{{TwoLegResult|[[Slavia Praga]]|CZE|1 - 3|'''[[VfB Stuttgart|Stoccarda]]'''|DEU|1 - 1|0 - 2|winner=2}}
{{TwoLegResult|[[AEK Atene]]|GRC|1 - 2|'''[[Lokomotiv Mosca]]'''|RUS|0 - 0|1 - 2|winner=2}}
{{TwoLegResult|[[Real Betis|Betis Siviglia]]|ESP|2 - 5|'''[[Chelsea F.C.|Chelsea]]'''|ENG|1 - 2|1 - 3|winner=2}}
|}
== Semifinale ==
{{TwoLegStart}}
{{TwoLegResult|[[Vicenza Calcio|Vicenza]]|ITA|2 - 3|'''[[Chelsea F.C.|Chelsea]]'''|ENG|1 - 0|1 - 3|winner=2}}
{{TwoLegResult|'''[[VfB Stuttgart|Stoccarda]]'''|DEU|3 - 1|[[Lokomotiv Mosca]]|RUS|2 - 1|1 - 0|winner=1}}
|}
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