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Pertandingan-pertandingan ini dimainkan pada [[13 Juli]] dan [[27 Juli]] 2006.
{{TwoLeg start}}
!colspan="5"|Wilayah Selatan dan Mediterania
{{TwoLegResult|[[NK Varteks]]|Kroasia|1-3|'''[[SK Tirana]]'''|Albania| 1-1 | 0-2 }}
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{{TwoLegResult|[[KS Dinamo Tirana]]|Albania|1-5|'''[[PFC CSKA Sofia]]'''|Bulgaria| 0-1 | 1-4 }}
{{TwoLegResult|[[FCNK KoperVarteks|Varteks]]|SloveniaKroasia|0-61–3|'''[[PFCKF Litex LovechTirana|Tirana]]'''|BulgariaAlbania| 0-1 1–1| 0-5 0–2}}
{{TwoLegResult|'''[[FKKS Dinamo SarajevoTirana|Dinamo Tirana]]|Albania|1–5|'''|Bosnia[[PFC danCSKA HerzegovinaSofia|5-0|[[FCCSKA Rànger'sSofia]]'''|AndorraBulgaria| 3-0 0–1| 2-0 1–4}}
{{TwoLegResult|[[HNKFC OrašjeKoper|Koper]]|Bosnia dan HerzegovinaSlovenia|0-70–6|'''[[NKPFC DomžaleLitex Lovech|Litex Lovech]]'''|SloveniaBulgaria| 0-2 0–1| 0-5 0–5}}
{{TwoLegResult|'''[[HiberniansFK F.C.Sarajevo|Sarajevo]]|Malta|1-9 |'''|BIH|5–0|[[DinamoFC Bucureşti]]'Rànger's|Rànger's]]|RomaniaAND| 0-4 3–0|1-5 2–0}}
{{TwoLegResult|'''[[APOELHNK FCOrašje|Orašje]]|BIH|0–7|'''|Cyprus|7-1|[[S.S.NK MurataDomžale|Domžale]]'''|San MarinoSlovenia| 3-1 0–2| 4-0 0–5}}
{{TwoLegResult|[[NKHibernians RijekaF.C.|Hibernians]]|KroasiaMLT|3-41–9|'''[[ACFC OmoniaDinamo Bucureşti|Dinamo Bucureşti]]'''|CyprusROU| 2-2 0–4| 1-2 1–5}}
{{TwoLegResult|'''[[PFCAPOEL Lokomotiv SofiaF.C.|APOEL]]'''|BulgariaCYP|3-17–1|[[FKS.S. Makedonija Gorce PetrovMurata|Murata]]|MakedoniaSMR| 2-0 3–1| 1-1 4–0}}
{{TwoLegResult|[[FKNK VardarRijeka|Rijeka]]|MakedoniaKroasia|2-7 3–4|'''[[K.S.V.AC RoeselareOmonia|Omonia]]'''|BelgiumCYP| 1-2 2–2|1-5 1–2}}
{{TwoLegResult|'''[[RapidPFC BucureştiLokomotiv Sofia|Lokomotiv Sofia]]'''|RomaniaBulgaria|6-03–1|[[SliemaFK WanderersMakedonija F.C.Gjorče Petrov|Makedonija Gjorče Petrov]]|MaltaMKD| 5-0 2–0| 1-0 1–1}}
{{TwoLegResult|[[ÚjpestFK FCVardar|Vardar]]|HungariaMKD|1-42–7|'''[[FCK.S.V. VaduzRoeselare|Roeselare]]'''|LiechtensteinBEL| 0-4 1–2| 1-0 1–5}}
{{TwoLegResult|'''[[FC ZimbruRapid ChişinăuBucureşti|Rapid Bucureşti]]'''|MoldovaROU|3-26–0|[[FKSliema KarabakhWanderers F.C.|Sliema Wanderers]]|AzerbaijanMLT| 1-1 5–0| 2-1([[extra time|aet]]) 1–0}}
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{{TwoLegResult|[[FC MIKA]]|Armenia|1-4|'''[[BSC Young Boys]]'''|Swiss| 1-3 | 0-1 }}
!colspan="5"|Wilayah Tengah dan Timur
{{TwoLegResult|'''[[Videoton FC Fehérvár]]'''|Hungaria|([[Away goals rule|a]])2-2|[[FC Kairat Almaty]]|Kazakhstan| 1-0 | 1-2 }}
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{{TwoLegResult|[[Zagłębie Lubin]]|Poland|1-1([[Away goals rule|a]])|'''[[F.C. Dinamo Minsk]]'''|Belarus| 1-1 | 0-0 }}
{{TwoLegResult|'''[[FKÚjpest KarvanFC|Újpest]]|HUN|1–4|'''|Azerbaijan|2-0|[[FC Spartak TrnavaVaduz|Vaduz]]'''|SlovakiaLIE| 1-0 0–4| 1-0 1–0}}
{{TwoLegResult|'''[[FC AmeriZimbru TbilisiChişinău|Zimbru Chişinău]]'''|GeorgiaMDA|3–2|([[AwayFK goals ruleKarabakh|aKarabakh]])2-2|AZE|1–1|2–1([[FCextra Banantstime|aet]]|Armenia| 0-1 | 2-1 )}}
{{TwoLegResult|'''[[FC BATEMIKA|MIKA]]|ARM|1–4|'''|Belarus|3-0|[[FCBSC NistruYoung OtaciBoys|Young Boys]]'''|MoldovaSUI| 2-0 1–3| 1-0 0–1}}
{{TwoLegResult|'''[[FC BaselFehérvár|Videoton]]'''|SwissHUN|3-12–2 ([[Peraturan gol tandang|AGR]])|[[FC TobolKairat|Kairat]]|KazakhstanKAZ| 3-1 1–0| 0-0 1–2}}
{{TwoLegResult|'''[[FCZagłębie ArtmediaLubin]]|POL|1–1 Bratislava([[Peraturan gol tandang|AGR]])|'''|Slovakia|3-2|[[FC WITDinamo GeorgiaMinsk|Dinamo Minsk]]'''|GeorgiaBLR| 2-0 1–1| 1-2 0–0}}
{{TwoLegResult|[[HJK Helsinki]]|Finland|2-4|'''[[DroghedaFK UnitedKarvan|Karvan]]'''|IrlandiaAZE| 1-1 2–0| 1-3 ([[extraFC timeSpartak Trnava|aetSpartak Trnava]]) |SVK|1–0|1–0}}
{{TwoLegResult|'''[[BrøndbyFC IFAmeri Tbilisi|Ameri Tbilisi]]'''|DenmarkGEO|3-12–2 ([[Peraturan gol tandang|AGR]])|[[ValurFC Banants|Banants]]|IcelandARM| 3-1 0–1| 0-0 2–1}}
{{TwoLegResult|[[Gefle IF]]|Swedia|1-2|'''[[LlanelliFC A.F.C.BATE|BATE]]'''|WalesBLR|3–0|[[FC 1-2Nistru Otaci|Nistru 0-0 Otaci]]|MDA|2–0|1–0}}
{{TwoLegResult|'''[[JeunesseFC EschBasel|Basel]]'''|LuksemburgSUI|0-53–1|'''[[SkontoFC FCTobol|Tobol]]'''|LatviaKAZ| 0-2 3–1| 0-3 0–0}}
{{TwoLegResult|'''[[ÅtvidabergsFC FFArtmedia Petržalka|Artmedia]]'''|SwediaSVK|7-03–2|[[FC EtzellaWIT EttelbruckGeorgia|WIT Georgia]]|LuksemburgGEO| 4-0 2–0| 3-0 1–2}}
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{{TwoLegResult|'''[[FK Ventspils]]'''|Latvia|4-1|[[GÍ Gøta]]|the Faroe Islands| 2-1 | 2-0 }}
!colspan="5"|Wilayah utara
{{TwoLegResult|[[Glentoran F.C.]]|Irlandia Utara|0-2|'''[[S.K. Brann]]'''|Norway| 0-1 | 0-1 }} ▼|-
{{TwoLegResult|'''[[Randers FC]]'''|Denmark|([[Away goals rule|a]])2-2 |[[Íþróttabandalag Akraness|ÍA Akranes]]|Iceland| 1-0 | 1-2}} ▼{{TwoLegResult|[[PortadownHJK F.C.Helsinki]]|Irlandia UtaraFIN|1-42–4|'''[[FBKDrogheda KaunasUnited F.C.|Drogheda United]]'''|Lithuania| 1-3Republik Irlandia|1–1|1–3 0-1([[extra time|aet]])}}
{{TwoLegResult|'''[[RhylBrøndby F.C.IF|Brøndby]]'''|WalesDenmark|1-2 3–1|'''[[FK SūduvaValur]]'''|LithuaniaISL| 0-0 3–1|1-2 0–0}}
{{TwoLegResult|'''[[FCGefle Levadia TallinnIF|Gefle]]|Swedia|1–2|'''|Estonia|2-1|[[FCLlanelli HakaA.F.C.|Llanelli]]'''|FinlandWAL| 2-0 1–2| 0-1 0–0}}
{{TwoLegResult|[[SkálaJeunesse ÍFEsch]]|the Faroe IslandsLUX|0-40–5|'''[[I.K.Skonto StartFC|Skonto]]'''|NorwayLVA| 0-1 0–2| 0-3 0–3}}
{{TwoLegResult|'''[[F.C.Åtvidabergs Lyn Oslo]]FF|Norway|1-1([[Away goals rule|aÅtvidaberg]])|'''|Swedia|7–0|[[FC FloraEtzella TallinnEttelbruck|Etzella Ettelbruck]]'''|EstoniaLUX| 1-1 4–0| 0-0 3–0}}
{{TwoLegResult|'''[[IFKFK GöteborgVentspils|Ventspils]]'''|SwediaLVA|0-24–1|'''[[DerryGÍ City F.C.Gøta]]'''|Irlandia|Kepulauan 0-1 Faroe| 0-1 2–1|2–0}}
▲{{TwoLegResult|[[Glentoran F.C. |Glentoran]]| Irlandia UtaraNIR| 0-20–2|'''[[ S.K.SK Brann|Brann]]'''| NorwayNOR| 0-1 0–1| 0-1 0–1}}
▲{{TwoLegResult|'''[[Randers FC |Randers]]'''|Denmark| 2–2 ([[ AwayPeraturan goalsgol ruletandang| aAGR]]) 2-2 |[[Íþróttabandalag Akraness|ÍA Akranes]]| IcelandISL| 1-0 1–0| 1-21–2}}
{{TwoLegResult|[[Portadown F.C.|Portadown]]|NIR|1–4|'''[[FBK Kaunas|Kaunas]]'''|LTU|1–3|0–1}}
{{TwoLegResult|[[Rhyl F.C.|Rhyl]]|WAL|1–2|'''[[FK Sūduva Marijampolė|Sūduva]]'''|LTU|0–0|1–2}}
{{TwoLegResult|'''[[FC Levadia Tallinn|Levadia Tallinn]]'''|Estonia|2–1|[[FC Haka|Haka]]|FIN|2–0|0–1}}
{{TwoLegResult|[[Skála ÍF|Skála]]|Kepulauan Faroe|0–4|'''[[IK Start|Start]]'''|NOR|0–1|0–3}}
{{TwoLegResult|[[FC Lyn Oslo|Lyn Oslo]]|NOR|1–1 ([[Peraturan gol tandang|AGR]])|'''[[FC Flora Tallinn|Flora Tallinn]]'''|Estonia|1–1|0–0}}
{{TwoLegResult|[[IFK Göteborg]]|Swedia|0–2|'''[[Derry City F.C.|Derry City]]'''|Republik Irlandia|0–1|0–1}}
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