| date | stage | club1 | club2 | goals | |
| 2006-07-13 | Qualifying_Round_1 | Varteks_Varazdin(Croatia) | KF_Tirana(Albania) | 1 | 1 | - |
| 2006-07-13 | Qualifying_Round_1 | Dinamo_Tirana(Albania) | CSKA_Sofia(Bulgaria) | 0 | 1 | - |
| 2006-07-13 | Qualifying_Round_1 | NK_Koper(Slovenia) | Liteks_Lovech(Bulgaria) | 0 | 1 | - |
| 2006-07-13 | Qualifying_Round_1 | FK_Sarajevo(Bosnia-Herzegovina) | Rangers_FC(Andorra) | 3 | 0 | - |
| 2006-07-13 | Qualifying_Round_1 | NK_Orasje(Bosnia-Herzegovina) | NK_Domzale(Slovenia) | 0 | 2 | - |
| 2006-07-13 | Qualifying_Round_1 | Hibernians_FC(Malta) | Dinamo_Bucuresti(Romania) | 0 | 4 | - |
| 2006-07-13 | Qualifying_Round_1 | APOEL_Nicosia(Cyprus) | Murata(San-Marino) | 3 | 1 | - |
| 2006-07-13 | Qualifying_Round_1 | NK_Rijeka(Croatia) | Omonia_Nicosia(Cyprus) | 2 | 2 | - |
| 2006-07-13 | Qualifying_Round_1 | Lokomotiv_Sofia(Bulgaria) | Makedonija_Skopje(North_Macedonia) | 2 | 0 | - |
| 2006-07-13 | Qualifying_Round_1 | Vardar_Skopje(North_Macedonia) | KSV_Roeselare(Belgium) | 1 | 2 | - |
| 2006-07-13 | Qualifying_Round_1 | Rapid_Bucuresti(Romania) | Sliema_Wanderers(Malta) | 5 | 0 | - |
| 2006-07-13 | Qualifying_Round_1 | Ujpest_TE(Hungary) | FC_Vaduz(Liechtenstein) | 0 | 4 | - |
| 2006-07-13 | Qualifying_Round_1 | Zimbru_Chisinau(Moldova) | Qarabag_FK(Azerbaijan) | 1 | 1 | - |
| 2006-07-13 | Qualifying_Round_1 | Mika_Ashtarak(Armenia) | Young_Boys(Switzerland) | 1 | 3 | - |
| 2006-07-13 | Qualifying_Round_1 | Videoton_Fehervar(Hungary) | Kairat_Almaty(Kazakhstan) | 1 | 0 | - |
| 2006-07-13 | Qualifying_Round_1 | Zaglebie_Lubin(Poland) | Dinamo_Minsk(Belarus) | 1 | 1 | - |
| 2006-07-13 | Qualifying_Round_1 | Karvan_Evlakh(Azerbaijan) | Spartak_Trnava(Slovakia) | 1 | 0 | - |
| 2006-07-13 | Qualifying_Round_1 | Ameri_Tbilisi(Georgia) | Banants_Yerevan(Armenia) | 0 | 1 | - |
| 2006-07-13 | Qualifying_Round_1 | BATE_Borisov(Belarus) | Nistru_Otaci(Moldova) | 2 | 0 | - |
| 2006-07-13 | Qualifying_Round_1 | FC_Basel(Switzerland) | Tobol_Kustanai(Kazakhstan) | 3 | 1 | - |
| 2006-07-13 | Qualifying_Round_1 | Petrzalka_Bratislava(Slovakia) | Georgia_Tbilisi(Georgia) | 2 | 0 | - |
| 2006-07-13 | Qualifying_Round_1 | HJK_Helsinki(Finland) | Drogheda_United(Ireland) | 1 | 1 | - |
| 2006-07-13 | Qualifying_Round_1 | Brondby_IF(Denmark) | Valur_Reykjavik(Iceland) | 3 | 1 | - |
| 2006-07-13 | Qualifying_Round_1 | Gefle_IF(Sweden) | Llanelli_FC(Wales) | 1 | 2 | - |
| 2006-07-13 | Qualifying_Round_1 | Jeunesse_dEsch(Luxembourg) | Skonto_Riga(Latvia) | 0 | 2 | - |
| 2006-07-13 | Qualifying_Round_1 | Atvidabergs_FF(Sweden) | Etzella_Ettelbruck(Luxembourg) | 4 | 0 | - |
| 2006-07-13 | Qualifying_Round_1 | FK_Ventspils(Latvia) | GI_Gotu(Faroe Islands) | 2 | 1 | - |
| 2006-07-13 | Qualifying_Round_1 | Glentoran(Northern Ireland) | SK_Brann_Bergen(Norway) | 0 | 1 | - |
| 2006-07-13 | Qualifying_Round_1 | Randers_Freia(Denmark) | IA_Akranes(Iceland) | 1 | 0 | - |
| 2006-07-13 | Qualifying_Round_1 | Portadown(Northern Ireland) | FBK_Kaunas(Lithuania) | 1 | 3 | - |
| 2006-07-13 | Qualifying_Round_1 | Rhyl_FC(Wales) | Suduva_Marijampole(Lithuania) | 0 | 0 | - |
| 2006-07-13 | Qualifying_Round_1 | Levadia_Tallinn(Estonia) | Haka_Valkeakoski(Finland) | 2 | 0 | - |
| 2006-07-13 | Qualifying_Round_1 | Skala_IF(Faroe Islands) | Start_Kristiansand(Norway) | 0 | 1 | - |
| 2006-07-13 | Qualifying_Round_1 | Lyn_Oslo(Norway) | Flora_Tallinn(Estonia) | 1 | 1 | - |
| 2006-07-13 | Qualifying_Round_1 | IFK_Goteborg(Sweden) | Derry_City(Ireland) | 0 | 1 | - |
| 2006-07-27 | Qualifying_Round_1 | KF_Tirana(Albania) | Varteks_Varazdin(Croatia) | 2 | 0 | - |
| 2006-07-27 | Qualifying_Round_1 | CSKA_Sofia(Bulgaria) | Dinamo_Tirana(Albania) | 4 | 1 | - |
| 2006-07-27 | Qualifying_Round_1 | Liteks_Lovech(Bulgaria) | NK_Koper(Slovenia) | 5 | 0 | - |
| 2006-07-27 | Qualifying_Round_1 | Rangers_FC(Andorra) | FK_Sarajevo(Bosnia-Herzegovina) | 0 | 2 | - |
| 2006-07-27 | Qualifying_Round_1 | NK_Domzale(Slovenia) | NK_Orasje(Bosnia-Herzegovina) | 5 | 0 | - |
| 2006-07-27 | Qualifying_Round_1 | Dinamo_Bucuresti(Romania) | Hibernians_FC(Malta) | 5 | 1 | - |
| 2006-07-27 | Qualifying_Round_1 | Murata(San-Marino) | APOEL_Nicosia(Cyprus) | 0 | 4 | - |
| 2006-07-27 | Qualifying_Round_1 | Omonia_Nicosia(Cyprus) | NK_Rijeka(Croatia) | 2 | 1 | - |
| 2006-07-27 | Qualifying_Round_1 | Makedonija_Skopje(North_Macedonia) | Lokomotiv_Sofia(Bulgaria) | 1 | 1 | - |
| 2006-07-27 | Qualifying_Round_1 | KSV_Roeselare(Belgium) | Vardar_Skopje(North_Macedonia) | 5 | 1 | - |
| 2006-07-27 | Qualifying_Round_1 | Sliema_Wanderers(Malta) | Rapid_Bucuresti(Romania) | 0 | 1 | - |
| 2006-07-27 | Qualifying_Round_1 | FC_Vaduz(Liechtenstein) | Ujpest_TE(Hungary) | 0 | 1 | - |
| 2006-07-27 | Qualifying_Round_1 | Qarabag_FK(Azerbaijan) | Zimbru_Chisinau(Moldova) | 1 | 2 | extra_time |
| 2006-07-27 | Qualifying_Round_1 | Young_Boys(Switzerland) | Mika_Ashtarak(Armenia) | 1 | 0 | - |
| 2006-07-27 | Qualifying_Round_1 | Kairat_Almaty(Kazakhstan) | Videoton_Fehervar(Hungary) | 2 | 1 | - |
| 2006-07-27 | Qualifying_Round_1 | Dinamo_Minsk(Belarus) | Zaglebie_Lubin(Poland) | 0 | 0 | - |
| 2006-07-27 | Qualifying_Round_1 | Spartak_Trnava(Slovakia) | Karvan_Evlakh(Azerbaijan) | 0 | 1 | - |
| 2006-07-27 | Qualifying_Round_1 | Banants_Yerevan(Armenia) | Ameri_Tbilisi(Georgia) | 1 | 2 | - |
| 2006-07-27 | Qualifying_Round_1 | Nistru_Otaci(Moldova) | BATE_Borisov(Belarus) | 0 | 1 | - |
| 2006-07-27 | Qualifying_Round_1 | Tobol_Kustanai(Kazakhstan) | FC_Basel(Switzerland) | 0 | 0 | - |
| 2006-07-27 | Qualifying_Round_1 | Georgia_Tbilisi(Georgia) | Petrzalka_Bratislava(Slovakia) | 2 | 1 | - |
| 2006-07-27 | Qualifying_Round_1 | Drogheda_United(Ireland) | HJK_Helsinki(Finland) | 3 | 1 | extra_time |
| 2006-07-27 | Qualifying_Round_1 | Valur_Reykjavik(Iceland) | Brondby_IF(Denmark) | 0 | 0 | - |
| 2006-07-27 | Qualifying_Round_1 | Llanelli_FC(Wales) | Gefle_IF(Sweden) | 0 | 0 | - |
| 2006-07-27 | Qualifying_Round_1 | Skonto_Riga(Latvia) | Jeunesse_dEsch(Luxembourg) | 3 | 0 | - |
| 2006-07-27 | Qualifying_Round_1 | Etzella_Ettelbruck(Luxembourg) | Atvidabergs_FF(Sweden) | 0 | 3 | - |
| 2006-07-27 | Qualifying_Round_1 | GI_Gotu(Faroe Islands) | FK_Ventspils(Latvia) | 0 | 2 | - |
| 2006-07-27 | Qualifying_Round_1 | SK_Brann_Bergen(Norway) | Glentoran(Northern Ireland) | 1 | 0 | - |
| 2006-07-27 | Qualifying_Round_1 | IA_Akranes(Iceland) | Randers_F?(Denmark) | 2 | 1 | - |
| 2006-07-27 | Qualifying_Round_1 | FBK_Kaunas(Lithuania) | Portadown(Northern Ireland) | 1 | 0 | - |
| 2006-07-27 | Qualifying_Round_1 | Suduva_Marijampole(Lithuania) | Rhyl_FC(Wales) | 2 | 1 | - |
| 2006-07-27 | Qualifying_Round_1 | Haka_Valkeakoski(Finland) | Levadia_Tallinn(Estonia) | 1 | 0 | - |
| 2006-07-27 | Qualifying_Round_1 | Start_Kristiansand(Norway) | Skala_IF(Faroe Islands) | 3 | 0 | - |
| 2006-07-27 | Qualifying_Round_1 | Flora_Tallinn(Estonia) | Lyn_Oslo(Norway) | 0 | 0 | - |
| 2006-07-27 | Qualifying_Round_1 | Derry_City(Ireland) | IFK_Goteborg(Sweden) | 1 | 0 | - |
| 2006-08-10 | Qualifying_Round_2 | APOEL_Nicosia(Cyprus) | Trabzonspor(Turkey) | 1 | 1 | - |
| 2006-08-10 | Qualifying_Round_2 | Hapoel_Tel-Aviv(Israel) | NK_Domzale(Slovenia) | 1 | 2 | - |
| 2006-08-10 | Qualifying_Round_2 | CSKA_Sofia(Bulgaria) | Hajduk_Kula(Serbia) | 0 | 0 | - |
| 2006-08-10 | Qualifying_Round_2 | KSV_Roeselare(Belgium) | Ethnikos_Achna(Cyprus) | 2 | 1 | - |
| 2006-08-08 | Qualifying_Round_2 | OFK_Belgrade(Serbia) | AJ_Auxerre(France) | 1 | 0 | - |
| 2006-08-10 | Qualifying_Round_2 | Dinamo_Bucuresti(Romania) | Beitar_Jerusalem(Israel) | 1 | 0 | - |
| 2006-08-10 | Qualifying_Round_2 | Partizan_Belgrade(Serbia) | NK_Maribor(Slovenia) | 2 | 1 | - |
| 2006-08-10 | Qualifying_Round_2 | FK_Sarajevo(Bosnia-Herzegovina) | Rapid_Bucuresti(Romania) | 1 | 0 | - |
| 2006-08-10 | Qualifying_Round_2 | Bnei_Yehuda(Israel) | Lokomotiv_Sofia(Bulgaria) | 0 | 2 | - |
| 2006-08-08 | Qualifying_Round_2 | Omonia_Nicosia(Cyprus) | Liteks_Lovech(Bulgaria) | 0 | 0 | - |
| 2006-08-10 | Qualifying_Round_2 | KF_Tirana(Albania) | Kayserispor(Turkey) | 0 | 2 | - |
| 2006-08-10 | Qualifying_Round_2 | Petrzalka_Bratislava(Slovakia) | Dinamo_Minsk(Belarus) | 2 | 1 | - |
| 2006-08-10 | Qualifying_Round_2 | SV_Ried(Austria) | FC_Sion(Switzerland) | 0 | 0 | - |
| 2006-08-10 | Qualifying_Round_2 | Videoton_Fehervar(Hungary) | Grasshoppers_Zurich(Switzerland) | 1 | 1 | - |
| 2006-08-10 | Qualifying_Round_2 | Karvan_Evlakh(Azerbaijan) | Slavia_Praha(Czech Republic) | 0 | 2 | - |
| 2006-08-10 | Qualifying_Round_2 | Chornomorets_Odesa(Ukraine) | Wisla_Plock(Poland) | 0 | 0 | - |
| 2006-08-10 | Qualifying_Round_2 | FC_Basel(Switzerland) | FC_Vaduz(Liechtenstein) | 1 | 0 | - |
| 2006-08-10 | Qualifying_Round_2 | Zimbru_Chisinau(Moldova) | Metalurg_Zaporizhia(Ukraine) | 0 | 0 | - |
| 2006-08-10 | Qualifying_Round_2 | SV_Mattersburg(Austria) | Wisla_Krakow(Poland) | 1 | 1 | - |
| 2006-08-10 | Qualifying_Round_2 | Hertha_BSC(Germany) | Ameri_Tbilisi(Georgia) | 1 | 0 | - |
| 2006-08-10 | Qualifying_Round_2 | Rubin_Kazan(Russia) | BATE_Borisov(Belarus) | 3 | 0 | - |
| 2006-08-10 | Qualifying_Round_2 | Young_Boys(Switzerland) | Olympique_Marseille(France) | 3 | 3 | - |
| 2006-08-10 | Qualifying_Round_2 | Start_Kristiansand(Norway) | Drogheda_United(Ireland) | 1 | 0 | - |
| 2006-08-10 | Qualifying_Round_2 | OB_Odense(Denmark) | Llanelli_FC(Wales) | 1 | 0 | - |
| 2006-08-10 | Qualifying_Round_2 | Randers_F?(Denmark) | FBK_Kaunas(Lithuania) | 3 | 1 | - |
| 2006-08-10 | Qualifying_Round_2 | FC_Twente_Enschede(Netherlands) | Levadia_Tallinn(Estonia) | 1 | 1 | - |
| 2006-08-10 | Qualifying_Round_2 | FK_Ventspils(Latvia) | Newcastle_United(England) | 0 | 1 | - |
| 2006-08-10 | Qualifying_Round_2 | SK_Brann_Bergen(Norway) | Atvidabergs_FF(Sweden) | 3 | 3 | - |
| 2006-08-10 | Qualifying_Round_2 | Molde_FK(Norway) | Skonto_Riga(Latvia) | 0 | 0 | - |
| 2006-08-10 | Qualifying_Round_2 | Flora_Tallinn(Estonia) | Brondby_IF(Denmark) | 0 | 0 | - |
| 2006-08-10 | Qualifying_Round_2 | Suduva_Marijampole(Lithuania) | Club_Brugge(Belgium) | 0 | 2 | - |
| 2006-08-10 | Qualifying_Round_2 | Gretna_FC(Scotland) | Derry_City(Ireland) | 1 | 5 | - |
| 2006-08-24 | Qualifying_Round_2 | Trabzonspor(Turkey) | APOEL_Nicosia(Cyprus) | 1 | 0 | - |
| 2006-08-24 | Qualifying_Round_2 | NK_Domzale(Slovenia) | Hapoel_Tel-Aviv(Israel) | 0 | 3 | - |
| 2006-08-24 | Qualifying_Round_2 | Hajduk_Kula(Serbia) | CSKA_Sofia(Bulgaria) | 1 | 1 | - |
| 2006-08-24 | Qualifying_Round_2 | Ethnikos_Achna(Cyprus) | KSV_Roeselare(Belgium) | 5 | 0 | - |
| 2006-08-24 | Qualifying_Round_2 | AJ_Auxerre(France) | OFK_Belgrade(Serbia) | 5 | 1 | - |
| 2006-08-24 | Qualifying_Round_2 | Beitar_Jerusalem(Israel) | Dinamo_Bucuresti(Romania) | 1 | 1 | - |
| 2006-08-24 | Qualifying_Round_2 | NK_Maribor(Slovenia) | Partizan_Belgrade(Serbia) | 1 | 1 | - |
| 2006-08-24 | Qualifying_Round_2 | Rapid_Bucuresti(Romania) | FK_Sarajevo(Bosnia-Herzegovina) | 2 | 0 | - |
| 2006-08-24 | Qualifying_Round_2 | Lokomotiv_Sofia(Bulgaria) | Bnei_Yehuda(Israel) | 4 | 0 | - |
| 2006-08-24 | Qualifying_Round_2 | Liteks_Lovech(Bulgaria) | Omonia_Nicosia(Cyprus) | 2 | 1 | - |
| 2006-08-24 | Qualifying_Round_2 | Kayserispor(Turkey) | KF_Tirana(Albania) | 3 | 1 | - |
| 2006-08-24 | Qualifying_Round_2 | Dinamo_Minsk(Belarus) | Petrzalka_Bratislava(Slovakia) | 2 | 3 | - |
| 2006-08-24 | Qualifying_Round_2 | FC_Sion(Switzerland) | SV_Ried(Austria) | 1 | 0 | - |
| 2006-08-24 | Qualifying_Round_2 | Grasshoppers_Zurich(Switzerland) | Videoton_Fehervar(Hungary) | 2 | 0 | - |
| 2006-08-24 | Qualifying_Round_2 | Slavia_Praha(Czech Republic) | Karvan_Evlakh(Azerbaijan) | 0 | 0 | - |
| 2006-08-24 | Qualifying_Round_2 | Wisla_Plock(Poland) | Chornomorets_Odesa(Ukraine) | 1 | 1 | - |
| 2006-08-24 | Qualifying_Round_2 | FC_Vaduz(Liechtenstein) | FC_Basel(Switzerland) | 2 | 1 | - |
| 2006-08-24 | Qualifying_Round_2 | Metalurg_Zaporizhia(Ukraine) | Zimbru_Chisinau(Moldova) | 3 | 0 | - |
| 2006-08-24 | Qualifying_Round_2 | Wisla_Krakow(Poland) | SV_Mattersburg(Austria) | 1 | 0 | - |