| ROUND | C | Q1 | Q2 | Q3 | R1 | R2 | QF | SF | F | |||||||||||
| l1 | l2 | l1 | l2 | l1 | l2 | r1 | r2 | r3 | r4 | r5 | r6 | l1 | l2 | l1 | l2 | l1 | l2 | |||
| Season archive |
| Tuesday, 25 July 2006 | ||||||
| q2l1 |  Ekranas | 1-4 | Dinamo Zagreb | |||
| Wednesday, 26 July 2006 | ||||||
| q2l1 |  Fenerbahçe | 4-0 | B36 | |||
| q2l1 |  Hearts | 3-0 | Široki Brijeg | |||
| q2l1 |  FC København | 2-0 | MyPa | |||
| q2l1 |  Levski | 2-0 | Sioni | |||
| q2l1 |  Cork City | 0-1 | Crvena Zvezda | |||
| q2l1 |  Debrecen | 1-1 | Rabotnički | |||
| q2l1 |  FC Zürich | 2-1 | FC Salzburg | |||
| q2l1 |  Djurgården | 1-0 | Ružomberok | |||
| q2l1 |  FH | 0-1 | Legia Warszawa | |||
| q2l1 |  Gorica | 0-2 | FCSB | |||
| q2l1 |  FK Liepāja | 1-4 | Dynamo | |||
| q2l1 |  Sheriff | 1-1 | Spartak | |||
| q2l1 |  Mladá Boleslav | 3-1 | Vålerenga | |||
| Tuesday, 1 August 2006 | ||||||
| q2l2 | B36 | 0-5 | Fenerbahçe | 0-9 | ||
| Wednesday, 2 August 2006 | ||||||
| q2l2 | MyPa | 2-2 | FC København | 2-4 | ||
| q2l2 | FCSB | 3-0 | Gorica | 5-0 | ||
| q2l2 | Spartak | 0-0 | Sheriff | 1-1 | ||
| q2l2 | Legia Warszawa | 2-0 | FH | 3-0 | ||
| q2l2 | FC Salzburg | 2-0 | FC Zürich | 3-2 | ||
| q2l2 | Dinamo Zagreb | 5-2 | Ekranas | 9-3 | ||
| q2l2 | Dynamo | 4-0 | FK Liepāja | 8-1 | ||
| q2l2 | Crvena Zvezda | 3-0 | Cork City | 4-0 | ||
| q2l2 | Vålerenga | 2-2 | Mladá Boleslav | 3-5 | ||
| q2l2 | Ružomberok | 3-1 | Djurgården | 3-2 | ||
| q2l2 | Rabotnički | 4-1 | Debrecen | 5-2 | ||
| q2l2 | Široki Brijeg | 0-0 | Hearts | 0-3 | ||
| q2l2 | Sioni | 0-2 | Levski | 0-4 | ||
