---- ---- ---- ---- ---- ---- ---- ---- ---- ---- The game was awarded 3–0 to Khazar Universiteti due to Schwarz-Weiß Bregenz fielding an ineligible player. ---- ---- ---- ---- ---- ---- ---- ---- ---- ----
Second leg
2–2 on aggregate, Sloboda Tuzla won on away goals rule. ---- The game was awarded 3–0 to Vllaznia due to Hapoel fielding an ineligible player. Vllaznia won 4–2 on aggregate. ---- Vardar won 10–2 on aggregate. ---- Slaven Belupo won 4–2 on aggregate. ---- Sartid won 11–0 on aggregate. ---- Marek Dupnitsa won 2–0 on aggregate. ---- Spartak Moscow won 2–1 on aggregate. ---- Teplice won 3–2 on aggregate. ---- Thun won 2–0 on aggregate. ---- Tescoma Zlín won 4–3 on aggregate. ---- Khazar Universiteti won 5–1 on aggregate. ---- 4–4 on aggregate, Spartak Trnava won on away goals rule. ---- Dinamo Minsk won 2–1 on aggregate. ---- ZTS Dubnica won 4–0 on aggregate. ---- Gent won 3–1 on aggregate. ---- Cork City won 4–1 on aggregate. ---- Vėtra won 4–0 on aggregate. ---- Odense won 7–0 on aggregate. ---- 1–1 on aggregate, Tampere United won on away goals rule. ---- Dinaburg won 4–0 on aggregate. ---- Esbjerg won 7–1 on aggregate.
Tescoma Zlín won 3–0 on aggregate. ---- Vėtra won 2–1 on aggregate. ---- The game was awarded 3–0 to Genk due to Marek Dupnitsa fielding an ineligible player. Genk won 5–1 on aggregate. ---- Villarreal won 5–0 on aggregate. ---- Shinnik Yaroslavl won 4–1 on aggregate. ---- Slovan Liberec won 7–1 on aggregate. ---- Thun won 7–3 on aggregate. ---- OFK Beograd won 5–1 on aggregate. ---- Cork City won 1–0 on aggregate. ---- Esbjerg won 2–1 on aggregate. ---- Spartak Moscow won 5–1 on aggregate. ---- Tampere United won 3–1 on aggregate. ---- Dinamo Minsk won 4–3 on aggregate. ---- Spartak Trnava won 3–1 on aggregate. ---- 1–1 on aggregate. Vardar won 4–3 on penalties. ---- Slaven Belupo won 2–1 on aggregate.
4–4 on aggregate, Atlético Madrid won on away goals rule. ---- Nantes won 4–2 on aggregate. ---- 2–2 on aggregate, Genk won on away goals rule. ---- Hamburger SV won 5–3 on aggregate. ---- União de Leiria won 6–2 on aggregate. ---- Schalke 04 won 7–1 on aggregate. ---- Slovan Liberec won 2–1 on aggregate. ---- Lille won 4–3 on aggregate. ---- 2–2 on aggregate, Slaven Belupo won on away goals rule. ---- OFK Beograd won 1–0 on aggregate. ---- Villarreal won 3–2 on aggregate. ---- Esbjerg won 5–1 on aggregate.
Semi-finals
First leg
---- ---- ---- ---- ----
Second leg
Schalke 04 won 6–1 on aggregate. ---- Lille won 4–1 on aggregate. ---- União de Leiria won 2–0 on aggregate. ---- 2–2 on aggregate, Slovan Liberec won on away goals rule. ---- Villarreal won 2–0 on aggregate. ---- Atlético Madrid won 5–1 on aggregate.
Finals
First leg
---- ----
Second leg
Schalke 04 won 3–1 on aggregate. ---- 2–2 on aggregate. Villareal won 3–1 on penalties. ---- Lille won 2–0 on aggregate.
