| Tuesday 28th July 2009 | |||
| 1st Leg | |||
| Anderlecht | 5-0 | Sivasspor | |
| FK Aktobe Lento | 0-0 | Maccabi Haifa | |
| FK Baku | 0-0 | Levski Sofia | |
| Sparta Prague | 3-1 | Panathinaikos | |
| Wednesday 29th July 2009 | |||
| 1st Leg | |||
| Apoel Nicosia | 2-0 | Partizan Belgrade | |
| Celtic | 0-1 | Dinamo Moscow | |
| FC Copenhagen | 3-1 | Stabaek | |
| FC Zurich | 2-3 | NK Maribor | |
| FK Ventspils | 1-0 | BATE Borisov | |
| Levadia Tallinn | 0-1 | Debreceni VSC | |
| Salzburg | 1-1 | Dinamo Zagreb | |
| Shakhtar Donetsk | 2-2 | Timisoara | |
| Sheriff Tiraspol | 0-0 | Slavia Prague | |
| Slovan Bratislava | 0-2 | Olympiakos | |
| Sporting Lisbon | 0-0 | FC Twente Enschede | |
| Tuesday 4th August 2009 | |||
| 2nd Leg | |||
| Dinamo Zagreb | 1-2 | Salzburg | (2-3) |
| FC Twente Enschede | 1-1 | Sporting Lisbon | (1-1) |
| (Sporting Lisbon won on away goals) | |||
| Maccabi Haifa | 4-3 | FK Aktobe Lento | (4-3) |
| Panathinaikos | 3-0 | Sparta Prague | (4-3) |
| Sivasspor | 3-1 | Anderlecht | (3-6) |
| Wednesday 5th August 2009 | |||
| 2nd Leg | |||
| BATE Borisov | 2-1 | FK Ventspils | (2-2) |
| (FK Ventspils won on away goals) | |||
| Debreceni VSC | 1-0 | Levadia Tallinn | (2-0) |
| Dinamo Moscow | 0-2 | Celtic | (1-2) |
| Levski Sofia | 2-0 | FK Baku | (2-0) |
| NK Maribor | 0-3 | FC Zurich | (3-5) |
| Olympiakos | 2-0 | Slovan Bratislava | (4-0) |
| Partizan Belgrade | 1-0 | Apoel Nicosia | (1-2) |
| Slavia Prague | 1-1 | Sheriff Tiraspol | (1-1) |
| (Sheriff Tiraspol won on away goals) | |||
| Stabaek | 0-0 | FC Copenhagen | (1-3) |
| Timisoara | 0-0 | Shakhtar Donetsk | (2-2) |
| (Timisoara won on away goals) | |||
