| Tuesday 12th August 2008 | |||
| 1st Leg | |||
| Fiorentina | 2-0 | Slavia Prague | |
| Wednesday 13th August 2008 | |||
| 1st Leg | |||
| AaB Aalborg | 2-0 | FBK Kaunas | |
| Anorthosis Famagusta | 3-0 | Olympiakos | |
| Barcelona | 4-0 | Wisla Krakow | |
| FC Twente Enschede | 0-2 | Arsenal | |
| Galatasaray | 2-2 | Steaua Bucharest | |
| Juventus | 4-0 | Artmedia Petrzalka | |
| Levski Sofia | 0-1 | BATE Borisov | |
| Partizan Belgrade | 2-2 | Fenerbahce | |
| Schalke 04 | 1-0 | Atletico Madrid | |
| Shakhtar Donetsk | 2-0 | Dinamo Zagreb | |
| SK Brann | 0-1 | Marseille | |
| Sparta Prague | 1-2 | Panathinaikos | |
| Spartak Moscow | 1-4 | Dinamo Kiev | |
| Standard Liege | 0-0 | Liverpool | |
| Vitoria Guimaraes | 0-0 | Basle | |
| Tuesday 26th August 2008 | |||
| 2nd Leg | |||
| Artmedia Petrzalka | 1-1 | Juventus | (1-5) |
| Panathinaikos | 1-0 | Sparta Prague | (3-1) |
| Wisla Krakow | 1-0 | Barcelona | (1-4) |
| Wednesday 27th August 2008 | |||
| 2nd Leg | |||
| Arsenal | 4-0 | FC Twente Enschede | (6-0) |
| Atletico Madrid | 4-0 | Schalke 04 | (4-1) |
| Basle | 2-1 | Vitoria Guimaraes | (2-1) |
| BATE Borisov | 1-1 | Levski Sofia | (2-1) |
| Dinamo Kiev | 4-1 | Spartak Moscow | (8-2) |
| Dinamo Zagreb | 1-3 | Shakhtar Donetsk | (1-5) |
| FBK Kaunas | 0-2 | AaB Aalborg | (0-4) |
| Fenerbahce | 2-1 | Partizan Belgrade | (4-3) |
| Liverpool | 1-0 | Standard Liege | aet (1-0) |
| Marseille | 2-1 | SK Brann | (3-1) |
| Olympiakos | 1-0 | Anorthosis Famagusta | (1-3) |
| Slavia Prague | 0-0 | Fiorentina | (0-2) |
| Steaua Bucharest | 1-0 | Galatasaray | (3-2) |
