The qualifying rounds for the 2008–09 UEFA Champions League began on 15 July 2008. In total, there were three qualifying rounds which provided 16 clubs to join the group stages.
| Key to colours | |
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| Qualify for the group stage | |
| Eliminated in the Third qualifying round; Advanced to the UEFA Cup first round |
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The draw for the first qualifying round took place on 1 July 2008 in Nyon, Switzerland.
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Dinamo Zagreb won 3–1 on aggregate.----Artmedia Petržalka won 3–0 on aggregate.----Dinamo Tbilisi won 3–1 on aggregate.----FBK Kaunas won 7–2 on aggregate.----Göteborg won 9–0 on aggregate.----Ventspils won 4–1 on aggregate.----Anorthosis won 3–0 on aggregate.----1–1 on aggregate; Inter Baku won on away goals.----Tampere United won 3–2 on aggregate.----Domžale won 3–0 on aggregate.----Modriča won 4–1 on aggregate.----Sheriff won 4–1 on aggregate.----Drogheda United won 3–1 on aggregate.----BATE won 3–0 on aggregate.
The draw for the second qualifying round took place on 1 July 2008 in Nyon, Switzerland.
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FBK Kaunas won 2–1 on aggregate.----2–2 on aggregate; Brann won on away goals.----Partizan won 3–1 on aggregate.----Artmedia Petržalka won 7–3 on aggregate.----Anorthosis won 4–3 on aggregate.----Dinamo Zagreb won 6–2 on aggregate.----Panathinaikos won 3–0 on aggregate.----Basel won 5–3 on aggregate.----Sparta Prague won 3–0 on aggregate.----Dynamo Kyiv won 4–3 on aggregate.----BATE won 4–3 on aggregate.----Wisła Kraków won 6–2 on aggregate.----Fenerbahçe won 7–0 on aggregate.----Aalborg BK won 7–1 on aggregate.
The draw for the third qualifying round took place on 1 August 2008 in Nyon, Switzerland.
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Anorthosis won 3–1 on aggregate.----Basel won 2–1 on aggregate.----Shakhtar Donetsk won 5–1 on aggregate.----Atlético Madrid won 4–1 on aggregate.----Aalborg BK won 4–0 on aggregate.----Barcelona won 4–1 on aggregate.----BATE won 2–1 on aggregate.----Liverpool won 1–0 on aggregate.----Fenerbahçe won 4–3 on aggregate.----Arsenal won 6–0 on aggregate.----Dynamo Kyiv won 8–2 on aggregate.----Juventus won 5–1 on aggregate.----Marseille won 3–1 on aggregate.----Fiorentina won 2–0 on aggregate.----Steaua București won 3–2 on aggregate.----Panathinaikos won 3–1 on aggregate.