| Tuesday 25th July 2006 | |||
| 1st Leg | |||
| FK Ekranas Panevezys | 1-4 | Dinamo Zagreb | |
| Wednesday 26th July 2006 | |||
| 1st Leg | |||
| Cork City | 0-1 | Red Star Belgrade | |
| Debreceni VSC | 1-1 | Rabotnicki | |
| Djurgardens | 1-0 | Ruzomberok | |
| FC Copenhagen | 2-0 | MyPa-47 Anjalankoski | |
| FC Zurich | 2-1 | Salzburg | |
| Fenerbahce | 4-0 | B36 Torshavn | |
| FH Hafnarfjordur | 0-1 | Legia Warsaw | |
| Heart of Midlothian | 3-0 | NK Siroki Brijeg | |
| HIT Gorica | 0-2 | Steaua Bucharest | |
| Levski Sofia | 2-0 | Sioni Bolnisi | |
| Metalurgs Liepajas | 1-4 | Dinamo Kiev | |
| Mlada Boleslav | 3-1 | Valerenga | |
| Sheriff Tiraspol | 1-1 | Spartak Moscow | |
| Tuesday 1st August 2006 | |||
| 2nd Leg | |||
| B36 Torshavn | 0-5 | Fenerbahce | (0-9) |
| Wednesday 2nd August 2006 | |||
| 2nd Leg | |||
| Dinamo Kiev | 4-0 | Metalurgs Liepajas | (8-1) |
| Dinamo Zagreb | 5-2 | FK Ekranas Panevezys | (9-3) |
| Legia Warsaw | 2-0 | FH Hafnarfjordur | (3-0) |
| MyPa-47 Anjalankoski | 2-2 | FC Copenhagen | (2-4) |
| NK Siroki Brijeg | 0-0 | Heart of Midlothian | (0-3) |
| Rabotnicki | 4-1 | Debreceni VSC | (5-2) |
| Red Star Belgrade | 3-0 | Cork City | (4-0) |
| Ruzomberok | 3-1 | Djurgardens | (3-2) |
| Salzburg | 2-0 | FC Zurich | (3-2) |
| Sioni Bolnisi | 0-2 | Levski Sofia | (0-4) |
| Spartak Moscow | 0-0 | Sheriff Tiraspol | (1-1) |
| (Spartak Moscow won on away goals) | |||
| Steaua Bucharest | 3-0 | HIT Gorica | (5-0) |
| Valerenga | 2-2 | Mlada Boleslav | (3-5) |
