| 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, 11 July 2006 | ||||||
| q1l1 |  Linfield | 1-3 | Gorica | |||
| q1l1 |  Elbasani | 1-0 | Ekranas | |||
| q1l1 |  Birkirkara | 0-3 | B36 | |||
| q1l1 |  Pyunik | 0-0 | Sheriff | |||
| q1l1 |  F91 Düdelingen | 0-1 | Rabotnički | |||
| q1l1 |  TVMK | 2-3 | FH | |||
| q1l1 |  Sioni | 2-0 | Baki | |||
| Wednesday, 12 July 2006 | ||||||
| q1l1 |  MyPa | 1-0 | The New Saints | |||
| q1l1 |  Cork City | 1-0 | Apollon | |||
| q1l1 |  FK Liepāja | 1-0 | Aktobe | |||
| q1l1 |  Shakhter | 0-1 | Široki Brijeg | |||
| Tuesday, 18 July 2006 | ||||||
| q1l2 | Sheriff | 2-0 | Pyunik | 2-0 | ||
| q1l2 | Ekranas | 3-0 | Elbasani | 3-1 | ||
| q1l2 | Rabotnički | 0-0 | F91 Düdelingen | 1-0 | ||
| q1l2 | Baki | 1-0 | Sioni | 1-2 | ||
| Wednesday, 19 July 2006 | ||||||
| q1l2 | FH | 1-1 | TVMK | 4-3 | ||
| q1l2 | Gorica | 2-2 | Linfield | 5-3 | ||
| q1l2 | B36 | 2-2 | Birkirkara | 5-2 | ||
| q1l2 | Apollon | 1-1 | Cork City | 1-2 | ||
| q1l2 | The New Saints | 0-1 | MyPa | 0-2 | ||
| q1l2 | Široki Brijeg | 1-0 | Shakhter | 2-0 | ||
| q1l2 | Aktobe | 1-1 | FK Liepāja | 1-2 | ||
