| Tuesday 26th July 2011 | |||
| 1st Leg | |||
| Apoel Nicosia | 0-0 | Slovan Bratislava | |
| Dinamo Kiev | 0-2 | Rubin Kazan | |
| FC Twente Enschede | 2-0 | Vaslui | |
| FK Ekranas Panevezys | 0-0 | BATE Borisov | |
| Genk | 2-1 | Partizan Belgrade | |
| Liteks Lovech | 1-2 | Wisla Krakow | |
| Rangers | 0-1 | Malmo | |
| Zestafoni | 1-1 | Sturm Graz | |
| Wednesday 27th July 2011 | |||
| 1st Leg | |||
| Benfica | 2-0 | Trabzonspor | |
| FC Copenhagen | 1-0 | Shamrock Rovers | |
| HJK Helsinki | 1-2 | Dinamo Zagreb | |
| Maccabi Haifa | 2-1 | NK Maribor | |
| OB Odense | 1-1 | Panathinaikos | |
| Rosenborg | 0-1 | Viktoria Plzen | |
| Standard Liege | 1-1 | FC Zurich | |
| Tuesday 2nd August 2011 | |||
| 2nd Leg | |||
| BATE Borisov | 3-1 | FK Ekranas Panevezys | (3-1) |
| Panathinaikos | 3-4 | OB Odense | (4-5) |
| Shamrock Rovers | 0-2 | FC Copenhagen | (0-3) |
| Wednesday 3rd August 2011 | |||
| 2nd Leg | |||
| Dinamo Zagreb | 1-0 | HJK Helsinki | (3-1) |
| FC Zurich | 1-0 | Standard Liege | (2-1) |
| Malmo | 1-1 | Rangers | (2-1) |
| NK Maribor | 1-1 | Maccabi Haifa | (2-3) |
| Partizan Belgrade | 1-1 | Genk | (2-3) |
| Rubin Kazan | 2-1 | Dinamo Kiev | (4-1) |
| Slovan Bratislava | 0-2 | Apoel Nicosia | (0-2) |
| Sturm Graz | 1-0 | Zestafoni | (2-1) |
| Trabzonspor | 1-1 | Benfica | (1-3) |
| Vaslui | 0-0 | FC Twente Enschede | (0-2) |
| Viktoria Plzen | 3-2 | Rosenborg | (4-2) |
| Wisla Krakow | 3-1 | Liteks Lovech | (5-2) |
