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.
The draw for the first qualifying round took place on 1 July 2008.[1] The first legs were played on 17 July 2008 and the second legs were played on 29 and 31 July 2008.
In each region of the draw for the first qualifying round, teams were divided into two pots, on the basis of UEFA coefficients. The lower pots contained unranked teams from associations 34–53, together with Vėtra of Lithuania (the 33rd association). The higher pots contained teams from associations 1–32, together with Sūduva of Lithuania, and FH (who had a team ranking, 209).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 (Georgia, ranked 38) beat Spartak Trnava (Slovakia, 24); Vllaznia (Albania, 43) beat Koper (Slovenia, 29); and St Patrick's Athletic (Ireland, 35) beat Olimps (Latvia, 31).
|-!colspan="5"|Southern-Mediterranean region|-!colspan="5"|Central-East region|-!colspan="5"|Northern region|}
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
The draw for the second qualifying round was held on 1 August 2008 in Nyon, Switzerland,[2] 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. The first legs were played on 14 August 2008 and the second leg on 28 August 2008.
In each region of the draw for the second qualifying round, teams were divided into two pots, on the basis of 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 from the Central-East group to the Northern group. Furthermore, Liepājas Metalurgs and Sūduva were moved from the Northern group to the Central-East group, and Vaslui and Interblock Ljubljana were moved from the Southern-Mediterranean group to the Central-East group.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, Dnipro Dnipropetrovsk, Aris, Red Star Belgrade, Grasshopper, Slovan Liberec, Viking, Lokomotiv Sofia, IF Elfsborg, Gent, Queen of the South and Debrecen. St Patrick's Athletic 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|}
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