| Tuesday 12th July 2011 | |||
| 1st Leg | |||
| FK Mogren | 1-2 | Liteks Lovech | |
| NK Maribor | 2-0 | F91 Dudelange | |
| Pyunik Yerevan | 0-4 | Viktoria Plzen | |
| Shamrock Rovers | 1-0 | Flora Tallinn | |
| Slovan Bratislava | 2-0 | Tobol Kostanay | |
| Valletta | 2-3 | FK Ekranas Panevezys | |
| Wednesday 13th July 2011 | |||
| 1st Leg | |||
| Bangor City | 0-3 | HJK Helsinki | |
| Dinamo Zagreb | 3-0 | Neftchi Baku | |
| Linfield | 1-1 | BATE Borisov | |
| Maccabi Haifa | 5-1 | FK Borac | |
| Malmo | 2-0 | HB Torshavn | |
| Partizan Belgrade | 4-0 | Shkendija | |
| Rosenborg | 5-0 | Breidablik | |
| Skenderbeu | 0-2 | Apoel Nicosia | |
| Skonto Riga | 0-1 | Wisla Krakow | |
| Sturm Graz | 2-0 | Videoton FC Fehervar | |
| Zestafoni | 3-0 | Dacia | |
| Tuesday 19th July 2011 | |||
| 2nd Leg | |||
| BATE Borisov | 2-0 | Linfield | (3-1) |
| F91 Dudelange | 1-3 | NK Maribor | (1-5) |
| FK Ekranas Panevezys | 1-0 | Valletta | (4-2) |
| Flora Tallinn | 0-0 | Shamrock Rovers | (0-1) |
| HB Torshavn | 1-1 | Malmo | (1-3) |
| HJK Helsinki | 10-0 | Bangor City | (13-0) |
| Liteks Lovech | 3-0 | FK Mogren | (5-1) |
| Neftchi Baku | 0-0 | Dinamo Zagreb | (0-3) |
| Shkendija | 0-1 | Partizan Belgrade | (0-5) |
| Tobol Kostanay | 1-1 | Slovan Bratislava | (1-3) |
| Viktoria Plzen | 5-1 | Pyunik Yerevan | (9-1) |
| Wisla Krakow | 2-0 | Skonto Riga | (3-0) |
| Wednesday 20th July 2011 | |||
| 2nd Leg | |||
| Apoel Nicosia | 4-0 | Skenderbeu | (6-0) |
| Breidablik | 2-0 | Rosenborg | (2-5) |
| Dacia | 2-0 | Zestafoni | (2-3) |
| FK Borac | 3-2 | Maccabi Haifa | (4-7) |
| Videoton FC Fehervar | 3-2 | Sturm Graz | (3-4) |
