| Tuesday 14th July 2009 | |||
| 1st Leg | |||
| EB Streymur | 0-2 | Apoel Nicosia | |
| FK Ekranas Panevezys | 2-2 | FK Baku | |
| FK Makedonia Skopje | 0-2 | BATE Borisov | |
| Pyunik Yerevan | 0-0 | Dinamo Zagreb | |
| Rhyl | 0-4 | Partizan Belgrade | |
| Wednesday 15th July 2009 | |||
| 1st Leg | |||
| Debreceni VSC | 2-0 | Kalmar | |
| FC Copenhagen | 6-0 | FK Mogren | |
| FH Hafnarfjordur | 0-4 | FK Aktobe Lento | |
| FK Ventspils | 3-0 | F91 Dudelange | |
| Inter Turku | 0-1 | Sheriff Tiraspol | |
| Levski Sofia | 4-0 | Sant Julia | |
| Maccabi Haifa | 6-0 | Glentoran | |
| Salzburg | 1-1 | Bohemians | |
| SK Tirana | 1-1 | Stabaek | |
| Wisla Krakow | 1-1 | Levadia Tallinn | |
| WIT Georgia Tbilisi | 0-0 | NK Maribor | |
| Zrinjski Mostar | 1-0 | Slovan Bratislava | |
| Tuesday 21st July 2009 | |||
| 2nd Leg | |||
| Apoel Nicosia | 3-0 | EB Streymur | (5-0) |
| BATE Borisov | 2-0 | FK Makedonia Skopje | (4-0) |
| Dinamo Zagreb | 3-0 | Pyunik Yerevan | (3-0) |
| FK Baku | 4-2 | FK Ekranas Panevezys | (6-4) |
| Partizan Belgrade | 8-0 | Rhyl | (12-0) |
| Sant Julia | 0-5 | Levski Sofia | (0-9) |
| Sheriff Tiraspol | 1-0 | Inter Turku | (2-0) |
| Slovan Bratislava | 4-0 | Zrinjski Mostar | (4-1) |
| Stabaek | 4-0 | SK Tirana | (5-1) |
| Wednesday 22nd July 2009 | |||
| 2nd Leg | |||
| Bohemians | 0-1 | Salzburg | (1-2) |
| F91 Dudelange | 1-3 | FK Ventspils | (1-6) |
| FK Aktobe Lento | 2-0 | FH Hafnarfjordur | (6-0) |
| FK Mogren | 0-6 | FC Copenhagen | (0-12) |
| Glentoran | 0-4 | Maccabi Haifa | (0-10) |
| Kalmar | 3-1 | Debreceni VSC | (3-3) |
| (Debreceni VSC won on away goals) | |||
| Levadia Tallinn | 1-0 | Wisla Krakow | (2-1) |
| NK Maribor | 3-1 | WIT Georgia Tbilisi | (3-1) |
