| Tuesday 8th August 2006 | |||
| 1st Leg | |||
| Austria Vienna | 1-1 | Benfica | |
| Dinamo Zagreb | 0-3 | Arsenal | |
| Wednesday 9th August 2006 | |||
| 1st Leg | |||
| AC Milan | 1-0 | Red Star Belgrade | |
| CSKA Moscow | 3-0 | Ruzomberok | |
| Dinamo Kiev | 3-1 | Fenerbahce | |
| FC Copenhagen | 1-2 | Ajax | |
| Galatasaray | 5-2 | Mlada Boleslav | |
| Heart of Midlothian | 1-2 | AEK Athens | |
| Levski Sofia | 2-0 | Chievo | |
| Lille | 3-0 | Rabotnicki | |
| Liverpool | 2-1 | Maccabi Haifa | |
| Salzburg | 1-0 | Valencia | |
| Shakhtar Donetsk | 1-0 | Legia Warsaw | |
| Slovan Liberec | 0-0 | Spartak Moscow | |
| Standard Liege | 2-2 | Steaua Bucharest | |
| SV Hamburg | 0-0 | Osasuna | |
| Tuesday 22nd August 2006 | |||
| 2nd Leg | |||
| Benfica | 3-0 | Austria Vienna | (4-1) |
| Maccabi Haifa | 1-1 | Liverpool | (n) (2-3) |
| Osasuna | 1-1 | SV Hamburg | (1-1) |
| (SV Hamburg won on away goals) | |||
| Red Star Belgrade | 1-2 | AC Milan | (1-3) |
| Valencia | 3-0 | Salzburg | (3-1) |
| Wednesday 23rd August 2006 | |||
| 2nd Leg | |||
| AEK Athens | 3-0 | Heart of Midlothian | (5-1) |
| Ajax | 0-2 | FC Copenhagen | (2-3) |
| Arsenal | 2-1 | Dinamo Zagreb | (5-1) |
| Chievo | 2-2 | Levski Sofia | (2-4) |
| Fenerbahce | 2-2 | Dinamo Kiev | (3-5) |
| Legia Warsaw | 2-3 | Shakhtar Donetsk | (2-4) |
| Mlada Boleslav | 1-1 | Galatasaray | (3-6) |
| Rabotnicki | 0-1 | Lille | (0-4) |
| Ruzomberok | 0-2 | CSKA Moscow | (0-5) |
| Spartak Moscow | 2-1 | Slovan Liberec | (2-1) |
| Steaua Bucharest | 2-1 | Standard Liege | (4-3) |
