Beitar Jerusalem won 6–4 on aggregate. ---- Gent won 3–2 on aggregate. ---- Pogoń Szczecin won 9–2 on aggregate. ---- Budućnost Podgorica won 7–2 on aggregate. ---- Lokeren won 2–1 on aggregate. ---- Göteborg won 5–2 on aggregate. ---- Varteks won 5–3 on aggregate. ---- Slaven Belupo won 2–0 on aggregate. ---- Neuchâtel Xamax won 9–1 on aggregate. ---- CFR Ecomax Cluj won 7–3 on aggregate. ---- Gloria Bistrița won 16–0 on aggregate. ---- Tampere United won 3–0 on aggregate. ---- ZTS Dubnica won 2–0 on aggregate. ---- Žalgiris won 2–0 on aggregate. ---- Lech Poznań won 4–1 on aggregate. ---- Sturm Graz won 6–1 on aggregate. ---- Dinaburg won 4–1 on aggregate. ---- Pobeda won 3–1 on aggregate. ---- Tescoma Zlín won 1–0 on aggregate. ---- Lombard-Pápa won 3–1 on aggregate. ---- Inter Turku won 4–0 on aggregate.
Sigma Olomouc won 1–0 on aggregate. ---- 1–1 on aggregate, CFR Ecomax Cluj won in a penalty shootout. ---- Wolfsburg won 5–3 on aggregate. ---- Deportivo La Coruña won 4–2 on aggregate. ---- ZTS Dubnica won 4–1 on aggregate. ---- Slovan Liberec won 7–2 on aggregate. ---- Saint-Étienne won 3–2 on aggregate. ---- Gent won 1–0 on aggregate. ---- Hamburg won 8–2 on aggregate. ---- Slaven Belupo won 4–2 on aggregate. ---- Young Boys won 6–2 on aggregate. ---- Varteks won 6–5 on aggregate. ---- Tampere United won 1–0 on aggregate. ---- Göteborg won 4–2 on aggregate. ---- Žalgiris won 3–2 on aggregate. ---- Lens won 3–1 on aggregate.
Deportivo La Coruña won 4–0 on aggregate. ---- Žalgiris won 5–4 on aggregate. ---- 1–1 on aggregate, Sigma Olomouc won on away goals rule. ---- Marseille won 5–3 on aggregate. ---- Lens won 5–2 on aggregate. ---- 1–1 on aggregate, Roda won on away goals rule. ---- Hamburg won 3–0 on aggregate. ---- Valencia won 2–0 on aggregate. ---- Newcastle United won 5–1 on aggregate. ---- Lazio won 4–1 on aggregate. ---- Wolfsburg won 4–0 on aggregate. ---- 3–3 on aggregate, CFR Ecomax Cluj won on away goals rule.
Semi–finals
First leg
---- ---- ---- ---- ----
Second leg
CFR Ecomax Cluj won 7–2 on aggregate. ---- Lens won 4–0 on aggregate. ---- Valencia won 4–0 on aggregate. ---- Hamburg won 4–0 on aggregate. ---- Deportivo La Coruña won 4–2 on aggregate. ---- Marseille won 4–1 on aggregate.
Finals
First leg
---- ----
Second leg
Lens won 4–2 on aggregate. ---- Marseille won 5–3 on aggregate. ---- Hamburg won 1–0 on aggregate.
