| ROUND | Q1 | Q2 | R1 | R2 | R3 | R4 | QF | SF | F | |||||||||||
| l1 | l2 | l1 | l2 | l1 | l2 | r1 | r2 | r3 | r4 | r5 | l1 | l2 | l1 | l2 | l1 | l2 | l1 | l2 | ||
| Season archive |
| Tuesday, 8 August 2006 | ||||||
| q2l1 |  Omonia | 0-0 | Litex | |||
| q2l1 |  OFK Beograd | 1-0 | Auxerre | |||
| Thursday, 10 August 2006 | ||||||
| q2l1 | CSKA | 0-0 | Hajduk Kula | |||
| q2l1 |  Start | 1-0 | Drogheda United | |||
| q2l1 |  FC Twente | 1-1 | Levadia Tallinn | |||
| q2l1 |  Dinamo București | 1-0 | Beitar Jerusalem | |||
| q2l1 |  Young Boys | 3-3 | Marseille | |||
| q2l1 |  OB | 1-0 | Llanelli Town | |||
| q2l1 | Molde | 0-0 | Skonto | |||
| q2l1 | Brann | 3-3 | Åtvidaberg | |||
| q2l1 |  MOL Fehérvár | 1-1 | Grasshoppers | |||
| q2l1 |  Chornomorets | 0-0 | Wisła Płock | |||
| q2l1 |  Gretna | 1-5 | Derry City | |||
| q2l1 | Partizan | 2-1 | Maribor | |||
| q2l1 |  Hertha BSC Berlin | 1-0 | Ameri Tbilisi | |||
| q2l1 | APOEL | 1-1 | Trabzonspor | |||
| q2l1 | FC Basel | 1-0 | Vaduz | |||
| q2l1 |  SV Ried | 0-0 | Sion | |||
| q2l1 |  Tirana | 0-2 | Kayserispor | |||
| q2l1 | Hapoel Tel Aviv | 1-2 | Domžale | |||
| q2l1 |  FC Petrzalka 1898 | 2-1 | Dinamo Minsk | |||
| q2l1 |  Zimbru | 0-0 | Metalurh Zaporizhzhya* | |||
| q2l1 | Flora | 0-0 | Brøndby | |||
| q2l1 |  Roeselare | 2-1 | Ethnikos Achna | |||
| q2l1 | Bnei Yehuda | 0-2 | Lokomotiv Sofia | |||
| q2l1 |  Rubin | 3-0 | BATE | |||
| q2l1 |  Sarajevo | 1-0 | Rapid București | |||
| q2l1 | JFK Ventspils | 0-1 | Newcastle United | |||
| q2l1 | Randers | 3-1 | Kaunas | |||
| q2l1 | SV Mattersburg | 1-1 | Wisła Kraków | |||
| q2l1 | Sūduva | 0-2 | Club Brugge | |||
| q2l1 |  Karvan | 0-2 | Slavia Praha | |||
| Thursday, 24 August 2006 | ||||||
| q2l2 | Newcastle United | 0-0 | JFK Ventspils | 1-0 | ||
| q2l2 | Club Brugge | 5-2 | Sūduva | 7-2 | ||
| q2l2 | Brøndby | 4-0 | Flora | 4-0 | ||
| q2l2 | Marseille | 0-0 | Young Boys | 3-3 | ||
| q2l2 | Auxerre | 5-1 | OFK Beograd | 5-2 | ||
| q2l2 | Trabzonspor | 1-0 | APOEL | 2-1 | ||
| q2l2 | Grasshoppers | 2-0 | MOL Fehérvár | 3-1 | ||
| q2l2 | Sion | 1-0 | SV Ried | 1-0 | ||
| q2l2 | Rapid București | 2-0 | Sarajevo | 2-1 | ||
| q2l2 | Slavia Praha | 0-0 | Karvan | 2-0 | ||
| q2l2 | Skonto | 1-2 | Molde | 1-2 | ||
| q2l2 | Lokomotiv Sofia | 4-0 | Bnei Yehuda | 6-0 | ||
| q2l2 | Dinamo Minsk | 2-3 | FC Petrzalka 1898 | 3-5 | ||
| q2l2 | Beitar Jerusalem | 1-1 | Dinamo București | 1-2 | ||
| q2l2 | Maribor | 1-1 | Partizan | 2-3 | ||
| q2l2 | Litex | 2-1 | Omonia | 2-1 | ||
| q2l2 | Wisła Płock | 1-1 | Chornomorets | 1-1 | ||
| q2l2 | Åtvidaberg | 1-1 | Brann | 4-4 | ||
| q2l2 | Metalurh Zaporizhzhya* | 3-0 | Zimbru | 3-0 | ||
| q2l2 | Wisła Kraków | 1-0 | SV Mattersburg | 2-1 | ||
| q2l2 | Hajduk Kula | 1-1 | CSKA | 1-1, aet | ||
| q2l2 | Ethnikos Achna | 5-0 | Roeselare | 6-2 | ||
| q2l2 | BATE | 0-2 | Rubin | 0-5 | ||
| q2l2 | Kayserispor | 3-1 | Tirana | 5-1 | ||
| q2l2 | Vaduz | 2-1 | FC Basel | 2-2 | ||
| q2l2 | Domžale | 0-3 | Hapoel Tel Aviv | 2-4 | ||
| q2l2 | Derry City | 2-2 | Gretna | 7-3 | ||
| q2l2 | Llanelli Town | 1-5 | OB | 1-6 | ||
| q2l2 | Kaunas | 1-0 | Randers | 2-3 | ||
| q2l2 | Levadia Tallinn | 1-0 | FC Twente | 2-1 | ||
| q2l2 | Drogheda United | 1-0 | Start | 1-1, aet, p10-11 | ||
| q2l2 | Ameri Tbilisi | 2-2 | Hertha BSC Berlin | 2-3 | ||
