Baltika Kaliningrad won 5–1 on aggregate. ---- National București won 5–2 on aggregate. ---- Debrecen won 10–2 on aggregate. ---- Vojvodina won 5–3 on aggregate. ---- OD Trenčín won 5–2 on aggregate. ---- Makedonija GjP won 5–3 on aggregate. ---- Torpedo Kutaisi won 7–1 on aggregate. ---- Rimavská Sobota won 3–2 on aggregate. ---- Kongsvinger won 9–1 on aggregate. ---- Lyngby won 4–2 on aggregate. ---- Hradec Králové won 2–1 on aggregate. ---- Altay won 5–4 on aggregate. ---- TPS 3–3 Sion on aggregate. TPS won on away goals rule. ---- Inkaras Kaunas 1–1 Baki Fahlasi on aggregate. Inkaras Kaunas won 5–4 on penalties.
Second round
First leg
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Second leg
Werder Bremen won 5–1 on aggregate. ---- Sampdoria won 2–1 on aggregate. ---- Naţional București won 4–3 on aggregate. ---- Vojvodina won 4–0 on aggregate. ---- Bastia won 7–1 on aggregate. ---- Baltika Kaliningrad won 1–0 on aggregate. ---- Lommel 2–2 Torpedo Kutaisi on aggregate. Lommel won on away goals rule. ---- Austria Salzburg won 3–2 on aggregate. ---- Shinnik Yaroslavl won 5–2 on aggregate.
Debrecen won 3–2 on aggregate. ---- Sampdoria won 4–0 on aggregate. ---- Espanyol won 2–1 on aggregate. ---- Ruch Chorzów 2–2 Estrela da Amadora on aggregate. Ruch Chorzów won 4–2 on penalties. ---- Bologna 3–3 Naţional București on aggregate. Bologna won on away goals rule. ---- Valencia won 4–2 on aggregate. ---- Samsunspor won 4–0 on aggregate. ---- Fortuna Sittard won 5–2 on aggregate. ---- Bastia won 4–3 on aggregate. ---- Werder Bremen won 5–2 on aggregate. ---- Austria Salzburg won 5–3 on aggregate. ---- Vojvodina won 4–2 on aggregate.
Semi–finals
First leg
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Second leg
Vojvodina won 4–2 on aggregate. ---- Bologna won 3–2 on aggregate. ---- Austria Salzburg won 4–3 on aggregate. ---- Ruch Chorzów won 4–0 on aggregate. ---- Werder Bremen won 6–0 on aggregate. ---- Valencia won 3–0 on aggregate.
Finals
First leg
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Second leg
Valencia won 4–1 on aggregate. ---- Werder Bremen won 2–1 on aggregate. ---- Bologna won 3–0 on aggregate.
