The draw took place at UEFA headquarters in Nyon, Switzerland on 21 April 2008.

Based on the subsequent progress of the eleven co-winners in their UEFA Cup efforts, Braga was declared the outright winner of the Intertoto Cup.

Neftchi Baku won on away goals rule.

Locomotive Tbilisi 2–2 Etzella Ettelbruck on aggregate.

Etzella Ettelbruck won on away goals rule.

Saturn Moscow Oblast won 8–1 on aggregate.

Budapest Honvéd advanced on away goals rule.

The 11 winners entered the second qualifying round of the UEFA Cup.

Deportivo La Coruña won 3–1 on aggregate.

Eight of the eleven Intertoto Cup co-winners entered the UEFA Cup by winning their qualifying ties and progressed to the first round.

Five of those eight sides survived the first round and entered the Group stage.

Only Braga progressed to the round of 16, making them the overall winners.