3–3 on aggregate, St Patrick's Athletic won on away goals rule. ---- Lokeren won 5–4 on aggregate. ---- Santa Clara won 5–3 on aggregate. ---- BATE Borisov won 4–0 on aggregate. ---- Haka won 3–2 on aggregate. ---- Zürich won 8–2 on aggregate. ---- Gloria Bistrița won 2–0 on aggregate. ---- Slaven Belupo won 6–3 on aggregate. ---- Synot won 4–0 on aggregate. ---- Helsingborgs won 1–0 on aggregate. ---- Žalgiris won 1–0 on aggregate. ---- St. Gallen won 11–1 on aggregate. ---- Dinaburg won 2–1 on aggregate. ---- Ashdod won 6–1 on aggregate. ---- Bregenz won 5–1 on aggregate. ---- Levadia Tallinn won 4–2 on aggregate. ---- Teuta won 2–1 on aggregate. ---- Coleraine won 7–2 on aggregate. ---- Marek won 3–1 on aggregate. ---- FH won 4–3 on aggregate.
Slaven Belupo won 3–0 on aggregate. ---- Troyes won 4–2 on aggregate. ---- BATE Borisov won 5–0 on aggregate. ---- Villarreal won 4–2 on aggregate. ---- 1–1 on aggregate, Fulham won on away goals rule. ---- Sochaux won 4–1 on aggregate. ---- 3–3 on aggregate, Gent won on away goals rule. ---- Stuttgart won 3–0 on aggregate. ---- Torino won 2–1 on aggregate. ---- Krylia Sovetov won 4–0 on aggregate. ---- Teplice won 9–2 on aggregate. ---- Willem II won 2–1 on aggregate. ---- Zürich won 1–0 on aggregate. ---- Synot won 4–2 on aggregate. ---- Gloria Bistrița won 3–1 on aggregate. ---- Marek won 2–1 on aggregate.
3–3 on aggregate, Willem II won on away goals rule. ---- 1–1 on aggregate, Troyes won on away goals rule. ---- Stuttgart won 4–3 on aggregate. ---- Fulham won 2–1 on aggregate. ---- Lille won 3–0 on aggregate. ---- Teplice won 5–2 on aggregate. ---- Bologna won 2–0 on aggregate. ---- Málaga won 4–1 on aggregate. ---- Slaven Belupo won 6–1 on aggregate. ---- Sochaux won 3–0 on aggregate. ---- 2–2 aggregate. Villarreal won on penalties. ---- Aston Villa won 3–2 on aggregate.
Semi-finals
First leg
---- ---- ---- ---- ----
Second leg
Stuttgart won 3–1 on aggregate. ---- Bologna won 8–2 on aggregate. ---- The game was awarded 3–0 to Villareal due to Troyes fielding an ineligible player David Vairelles. Villarreal won 3–0 on aggregate. ---- Fulham won 3–0 on aggregate. ---- Málaga won 3–1 on aggregate. ---- Lille won 3–1 on aggregate.
Finals
First leg
---- ----
Second leg
Stuttgart won 2–1 on aggregate. ---- Fulham won 5–3 on aggregate. ---- Málaga won 2–1 on aggregate.