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== Turno preliminare ==
{{TwoLegStart}}
{{TwoLegResult|[[CS Tiligul-Tiras Tiraspol|Tiligul-Tiras Tiraspol]]|MDA|2 - 3|'''[[FC Sion|Sion]]'''|CHE|0 - 0|2 - 3|winner=2}}
{{TwoLegResult|[[Vác FC Samsung|Vác]]|HUN|2 - 4|'''[[FK Sileks Kratovo|Sileks Kratovo]]'''|MKD 1991-1995|1 - 1|1 - 3|winner=2}}
{{TwoLegResult|[[FC TPS Turku|TPS Turku]]|FIN|1 - 3|'''[[KS Teuta|Teuta]]'''|ALB|1 - 0|0 - 3|winner=2}}
{{TwoLegResult|[[FC Vaduz|Vaduz]]|LIE|1 - 14|'''[[SK Hradec Králové|Hradec Králové]]'''|CZE|0 - 5|1 - 9|winner=2}}
{{TwoLegResult|'''[[APOEL FC|Apoel Nicosia]]'''|CYP|3 - 0|[[PFC Neftchi|Neftchi]]|AZE|3 - 0|0 - 0|winner=1}}
{{TwoLegResult|[[Wrexham FC|Wrexham]]|WAL|0 - 1|'''[[Petrolul Ploiești]]'''|ROU|0 - 0|0 - 1|winner=2}}
{{TwoLegResult|[[Valletta FC|Valletta]]|MLT|2 - 5|'''[[FK Inter Bratislava|Inter Bratislava]]'''|SVK|0 - 0|2 - 5|winner=2}}
{{TwoLegResult|'''[[Shakhtar Donetsk]]'''|UKR|5 - 1|[[Linfield FC|Linfield]]|NIR|4 - 1|1 - 0|winner=1}}
{{TwoLegResult|'''[[FK Žalgiris Vilnius|Žalgiris Vilnius]]'''|LTU|3 - 2|[[NK Mura Murska Sobota|Mura Murska Sobota]]|SVN|2 - 0|1 - 2|winner=1}}
{{TwoLegResult|[[GKS Katowice|Katowice]]|POL|2 - 2|'''[[FC Ararat Yerevan|Ararat Yerevan]]'''|ARM|2 - 0|0 - 2 <small>(4-5 [[Tiri di rigore|dcr]])</small>|winner=2}}
{{TwoLegResult|[[FK Obilic|Obilic]]|SCG|2 - 3|'''[[FC Dinamo Batumi|Dinamo Batumi]]'''|GEO|0 - 1|2 - 2|winner=2}}
{{TwoLegResult|[[Derry City FC|Derry City]]|IRL|1 - 2|'''[[PFC Lokomotiv Sofia|Lokomotiv Sofia]]'''|BGR|1 - 0|0 - 2|winner=2}}
{{TwoLegResult|'''[[Maccabi Haifa FC|Maccabi Haifa]]'''|ISR|6 - 3|[[KÍ Klaksvík]]|FRO|4 - 0|2 - 3|winner=1}}
{{TwoLegResult|[[Dinamo-93 Minsk|Dynamo-93 Minsk]]|BLR|2 - 3|'''[[Molde FK|Molde]]'''|NOR|1 - 1|1 - 2|winner=2}}
{{TwoLegResult|[[CS Grevenmacher|Grevenmacher]]|LUX|3 - 4|'''[[Knattspyrnufélag Reykjavíkur|KR]]'''|ISL|3 - 2|0 - 2|winner=2}}
{{TwoLegResult|'''[[DAG-Liepaya]]'''|LVA|3 - 0|[[FC Lantana Tallinn|Lantana Tallinn]]|EST|3 - 0|0 - 0|winner=1}}
|}
== Sedicesimi di finale ==
{{TwoLegStart}}
{{TwoLegResult|[[FK Žalgiris Vilnius|Žalgiris Vilnius]]|LTU|2 - 3|'''[[Trabzonspor]]'''|TUR|2 - 2|0 - 1|winner=2}}
{{TwoLegResult|[[APOEL FC|Apoel Nicosia]]|CYP|0 - 8|'''[[Deportivo La Coruña]]'''|ESP|0 - 0|0 - 8|winner=2}}
{{TwoLegResult|[[FK Inter Bratislava|Inter Bratislava]]|SVK|1 - 5|'''[[Real Zaragoza]]'''|ESP|0 - 2|1 - 3|winner=2}}
{{TwoLegResult|'''[[Club Brugge]]'''|BEL|2 - 1|[[Shakhtar Donetsk]]|UKR|1 - 0|1 - 1|winner=1}}
{{TwoLegResult|[[PFC Lokomotiv Sofia|Lokomotiv Sofia]]|BGR|3 - 3|'''[[Halmstads BK]]'''|SWE|3 - 1|0 - 2|winner=2}}
{{TwoLegResult|[[KS Teuta|Teuta]]|ALB|0 - 4|'''[[Parma F.C.|Parma]]'''|ITA|0 - 2|0 - 2|winner=2}}
{{TwoLegResult|[[Molde F.K.|Molde]]|NOR|2 - 6|'''[[Paris Saint-Germain]]'''|FRA|2 - 3|0 - 3|winner=2}}
{{TwoLegResult|[[FC Dinamo Batumi|Dinamo Batumi]]|GEO|2 - 7|'''[[Celtic Glasgow]]'''|SCO|2 - 3|0 - 4|winner=2}}
{{TwoLegResult|'''[[Borussia Mönchengladbach]]'''|DEU|6 - 2|[[FK Sileks Kratovo|Sileks Kratovo]]|MKD 1991-1995|3 - 0|3 - 2|winner=1}}
{{TwoLegResult|'''[[AEK Atene]]'''|GRC|4 - 2|[[FC Sion|Sion]]|CHE|2 - 0|2 - 2|winner=1}}
{{TwoLegResult|[[Knattspyrnufélag Reykjavíkur|KR]]|ISL|3 - 6|'''[[Everton FC|Everton]]'''|ENG|2 - 3|1 - 3|winner=2}}
{{TwoLegResult|[[DAG-Liepaya]]|LVA|0 - 13|'''[[Feyenoord Rotterdam|Feyenoord]]'''|NLD|0 - 7|0 - 6|winner=2}}
{{TwoLegResult|'''[[FC Dynamo Mosca|Dynamo Mosca]]'''|RUS|4 - 1|[[FC Ararat Yerevan|Ararat Yerevan]]|ARM|3 - 1|1 - 0|winner=1}}
{{TwoLegResult|'''[[SK Hradec Králové|Hradec Králové]]'''|CZE|7 - 2|[[FC København|København]]|DNK|5 - 0|2 - 2|winner=1}}
{{TwoLegResult|'''[[Sporting Clube de Portugal|Sporting Lisbona]]'''|PRT|4 - 0|[[Maccabi Haifa FC|Maccabi Haifa]]|ISR|4 - 0|0 - 0|winner=1}}
{{TwoLegResult|'''[[SK Rapid Vienna|Rapid Vienna]]'''|AUT|3 - 1|[[Petrolul Ploiești]]|ROU|3 - 1|0 - 0|winner=1}}
|}
== Ottavi di finale ==
{{TwoLegStart}}
{{TwoLegResult|[[Trabzonspor]]|TUR|0 - 4|'''[[Deportivo La Coruña]]'''|ESP|0 - 1|0 - 3|winner=2}}
{{TwoLegResult|'''[[Real Zaragoza]]'''|ESP|3 - 1|[[Club Brugge]]|BEL|2 - 1|1 - 0|winner=1}}
{{TwoLegResult|[[Halmstads BK]]|SWE|3 - 4|'''[[Parma F.C.|Parma]]'''|ITA|3 - 0|0 - 4|winner=2}}
{{TwoLegResult|'''[[Paris Saint-Germain]]'''|FRA|4 - 0|[[Celtic Glasgow]]|SCO|1 - 0|3 - 0|winner=1}}
{{TwoLegResult|'''[[Borussia Mönchengladbach]]'''|DEU|5 - 1|[[AEK Atene]]|GRC|4 - 1|1 - 0|winner=1}}
{{TwoLegResult|[[Everton FC|Everton]]|ENG|0 - 1|'''[[Feyenoord Rotterdam|Feyenoord]]'''|NLD|0 - 0|0 - 1|winner=2}}
{{TwoLegResult|'''[[FC Dynamo Mosca|Dynamo Mosca]]'''|RUS|1 - 1|[[SK Hradec Králové|Hradec Králové]]|CZE|1 - 0|0 - 1 <small>(3-1 [[Tiri di rigore|dcr]])</small>|winner=1}}
{{TwoLegResult|[[Sporting Clube de Portugal|Sporting Lisbona]]|PRT|2 - 4|'''[[SK Rapid Vienna|Rapid Vienna]]'''|AUT|2 - 0|0 - 4 <small>([[Tempi supplementari|dts]])</small>|winner=2}}
|}
== Quarti di finale ==
{{TwoLegStart}}
{{TwoLegResult|'''[[Deportivo La Coruña]]'''|ESP|2 - 1|[[Real Zaragoza]]|ESP|1 - 0|1 - 1|winner=1}}
{{TwoLegResult|[[Parma F.C.|Parma]]|ITA|2 - 3|'''[[Paris Saint-Germain]]'''|FRA|1 - 0|1 - 3|winner=2}}
{{TwoLegResult|[[Borussia Mönchengladbach]]|DEU|2 - 3|'''[[Feyenoord Rotterdam|Feyenoord]]'''|NLD|2 - 2|0 - 1|winner=2}}
{{TwoLegResult|[[FC Dynamo Mosca|Dynamo Mosca]]|RUS|0 - 4|'''[[SK Rapid Vienna|Rapid Vienna]]'''|AUT|0 - 1|0 - 3|winner=2}}
|}
== Semifinali ==
{{TwoLegStart}}
{{TwoLegResult|[[Deportivo La Coruña]]|ESP|0 - 2|'''[[Paris Saint-Germain]]'''|FRA|0 - 1|0 - 1|winner=2}}
{{TwoLegResult|[[Feyenoord Rotterdam|Feyenoord]]|NLD|1 - 4|'''[[SK Rapid Vienna|Rapid Vienna]]'''|AUT|1 - 1|0 - 3|winner=2}}
|}
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