The qualifying rounds for the 2008–09 UEFA Cup began on 17 July 2008. In total, there were two qualifying rounds which narrowed clubs down to 80 teams in preparation for the first round.

First qualifying round

Summary

<section begin=Q1 /> The draw for the first qualifying round took place on 1 July 2008. The first legs were played on 17 July 2008 and the second legs were played on 29 and 31 July 2008.<section end=Q1 /> In each region of the draw for the first qualifying round, teams were divided into two pots, on the basis of [UEFA coefficients](https://bliptext.com/articles/uefa-coefficients). The lower pots contained unranked teams from associations 34–53, together with [Vėtra](https://bliptext.com/articles/fk-v-tra) of Lithuania (the 33rd association). The higher pots contained teams from associations 1–32, together with [Sūduva](https://bliptext.com/articles/fk-s-duva-marijampol) of Lithuania, and [FH](https://bliptext.com/articles/fh-men-s-football) (who had a team ranking, 209). <section begin=Q1 /> Three of the 37 ties were won by the team with the lower UEFA coefficient, all involving teams whose ranking was that of their association: [WIT Georgia](https://bliptext.com/articles/fc-wit-georgia) (Georgia, ranked 38) beat [Spartak Trnava](https://bliptext.com/articles/fc-spartak-trnava) (Slovakia, 24); [Vllaznia](https://bliptext.com/articles/ks-vllaznia-shkod-r) (Albania, 43) beat [Koper](https://bliptext.com/articles/fc-koper) (Slovenia, 29); and [St Patrick's Athletic](https://bliptext.com/articles/st-patrick-s-athletic-f-c) (Ireland, 35) beat [Olimps](https://bliptext.com/articles/jfk-olimps-r-ga) (Latvia, 31). !colspan="5"|Southern-Mediterranean region !colspan="5"|Central-East region !colspan="5"|Northern region <section end=Q1 />

Matches

Nordsjælland win 8–0 on aggregate Manchester City win 4–0 on aggregate St Patrick's Athletic win 3–0 on aggregate 2–2 on aggregate, Djurgården win on away goals Sūduva win 2–0 on aggregate Copenhagen win 11–0 on aggregate Haka win 6–2 on aggregate Midtjylland win 10–1 on aggregate Cherno More win 9–0 on aggregate APOEL win 1–0 on aggregate Zrinjski Mostar win 5–1 on aggregate Široki Brijeg win 3–1 on aggregate Ironi Kiryat Shmona win 4–1 on aggregate Vllaznia Shkodër win 2–1 on aggregate Ljubljana win 2–1 on aggregate Hapoel Tel Aviv win 5–0 on aggregate Hajduk Split win 7–0 on aggregate Omonia win 4–1 on aggregate Slaven Belupo win 8–0 on aggregate Salzburg win 10–0 on aggregate Győr win 3–2 on aggregate Bellinzona win 4–1 on aggregate Borac Čačak win 4–2 on aggregate Austria Wien win 2–1 on aggregate Hertha BSC win 8–1 on aggregate Lech Poznań win 5–1 on aggregate Legia Warszawa win 4–1 on aggregate WIT win 3–2 on aggregate MŠK Žilina win 3–2 on aggregate Debrecen win 2–1 on aggregate Vojvodina win 2–1 on aggregate FH win 8–3 on aggregate Viking win 2–1 on aggregate Kalmar win 10–1 on aggregate Honka win 4–2 on aggregate Liepājas Metalurgs win 3–1 on aggregate Brøndby win 3–0 on aggregate

Second qualifying round

Summary

<section begin=Q2 /> The draw for the second qualifying round was held on 1 August 2008 in [Nyon](https://bliptext.com/articles/nyon), Switzerland, and featured 16 teams entering directly at the second qualifying round, as well as the 37 winners from the previous round and the 11 third round winners of the [UEFA Intertoto Cup](https://bliptext.com/articles/2008-uefa-intertoto-cup). The first legs were played on 14 August 2008 and the second leg on 28 August 2008.<section end=Q2 /> In each region of the draw for the second qualifying round, teams were divided into two pots, on the basis of [UEFA coefficients](https://bliptext.com/articles/uefa-coefficients). The higher pots contained teams with a ranking of 176 or higher, and unranked teams from associations ranked 1 to 15 (or 17 in the Southern-Mediterranean region). As there were an odd number of teams in the Central and Northern groups in the 2nd qualifying round, UEFA moved [Rennes](https://bliptext.com/articles/stade-rennais-fc) from the Central-East group to the Northern group. Furthermore, [Liepājas Metalurgs](https://bliptext.com/articles/fk-liep-jas-metalurgs) and [Sūduva](https://bliptext.com/articles/fk-s-duva-marijampol) were moved from the Northern group to the Central-East group, and [Vaslui](https://bliptext.com/articles/cs-sporting-vaslui) and [Interblock Ljubljana](https://bliptext.com/articles/interblock-ljubljana) were moved from the Southern-Mediterranean group to the Central-East group. <section begin=Q2 /> 12 of the 32 ties were won by the team with the lower UEFA coefficient. The 12 teams that lost to a lower team were: [AEK Athens](https://bliptext.com/articles/aek-athens-f-c), [Dnipro Dnipropetrovsk](https://bliptext.com/articles/fc-dnipro), [Aris](https://bliptext.com/articles/aris-thessaloniki-f-c), [Red Star Belgrade](https://bliptext.com/articles/red-star-belgrade), [Grasshopper](https://bliptext.com/articles/grasshopper-club-zurich), [Slovan Liberec](https://bliptext.com/articles/fc-slovan-liberec), [Viking](https://bliptext.com/articles/viking-fk), [Lokomotiv Sofia](https://bliptext.com/articles/pfc-lokomotiv-sofia), [IF Elfsborg](https://bliptext.com/articles/if-elfsborg), [Gent](https://bliptext.com/articles/k-a-a-gent), [Queen of the South](https://bliptext.com/articles/queen-of-the-south-f-c) and [Debrecen](https://bliptext.com/articles/debreceni-vsc). [St Patrick's Athletic](https://bliptext.com/articles/st-patrick-s-athletic-f-c) were the only team to beat a higher-seeded team in each of the two qualifying rounds. !colspan="5"|Southern-Mediterranean region !colspan="5"|Central-East region !colspan="5"|Northern region <section end=Q2 />

Matches

Borac Čačak win 2–1 on aggregate Nordsjælland win 4–2 on aggregate Kalmar win 5–2 on aggregate 1–1 on aggregate, Manchester City win 4–2 on penalties Honka win 2–1 on aggregate Brøndby win 6–0 on aggregate Rennes win 3–2 on aggregate Copenhagen win 7–3 on aggregate St Patrick's win 4–3 on aggregate Aston Villa win 5–2 on aggregate Beşiktaş win 6–1 on aggregate Braga win 3–0 on aggregate Hapoel Tel Aviv win 3–0 on aggregate Slaven Belupo win 2–1 on aggregate Litex Lovech win 2–1 on aggregate Deportivo win 2–0 on aggregate APOEL 5–5 Red Star Belgrade on aggregate, APOEL win on away goals Napoli win 8–0 on aggregate Cherno More win 3–1 on aggregate Omonia win 3–2 on aggregate Vaslui win 5–1 on aggregate ''Zürich 2–2 Sturm Graz on aggregate. Zürich won 4–2 on penalties.'' VfB Stuttgart win 6–2 on aggregate Lech Poznań win 6–0 on aggregate Žilina win 4–2 on aggregate Match played as a one off in Austria due to political unrest in Georgia. Young Boys win 7–3 on aggregate FC Moscow win 4–1 on aggregate 4–4 on aggregate, Bellinzona win on away goals Hertha BSC win 3–0 on aggregate Salzburg win 4–2 on aggregate Rosenborg win 6–2 on aggregate