The qualifying rounds for the 2008–09 UEFA Cup began on 17 July 2008.
The draw for the first qualifying round took place on 1 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.
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/ASK (Latvia, 31).
St Patrick's Athletic won 3–0 on aggregate.
Ironi Kiryat Shmona won 4–1 on aggregate.
Hapoel Tel Aviv won 5–0 on aggregate.
Red Bull Salzburg won 10–0 on aggregate.
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 region).
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.
1–1 on aggregate; Manchester City won 4–2 on penalties.
St Patrick's Athletic won 4–3 on aggregate.
Hapoel Tel Aviv won 3–0 on aggregate.
Deportivo La Coruña won 2–0 on aggregate.
Red Bull Salzburg won 4–2 on aggregate.