| 1. Round | 18/09/2008 | Stade Rennais | - | FC Twente | 2:1 | ||||
| 1. Round | 02/10/2008 | FC Twente | - | Stade Rennais | 1:0 | ||||
| Group A | 23/10/2008 | FC Twente | - | Racing Santander | 1:0 | ||||
| Group A | 03/12/2008 | FC Twente | - | FC Schalke 04 | 2:1 |  |
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| Group A | 18/12/2008 | Paris Saint-Germain | - | FC Twente | 4:0 | ||||
| 3. Round | 19/02/2009 | Olympique Marseille | - | FC Twente | 0:1 | |
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| 3. Round | 26/02/2009 | FC Twente | - | Olympique Marseille | 6:7 pso |
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