The qualifying round matches of the 1999–2000 UEFA Cup were played on 12 and 26 August 2000. The round consisted of 38 matches.
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Shakhtar Donetsk won 4–3 on aggregate.----HJK Helsinki won 2–1 on aggregate.----Lokomotivi Tbilisi won 2–1 on aggregate.----1–1 on aggregate. Sigma Olomouc won on away goals.----Hapoel Tel Aviv won 4–1 on aggregate.----Red Star Belgrade won 4–2 on aggregate.----Spartak Trnava won 3–1 on aggregate.----Lokomotiv Moscow won 12–1 on aggregate.----Torpedo Kutaisi won 9–2 on aggregate.--------Gorica won 2–1 on aggregate.----Vojvodina won 5–1 on aggregate.----Club Brugge won 5–0 on aggregate.----Omonia won 8–1 on aggregate.----Kryvbas Kryvyi Rih won 5–0 on aggregate.----GAK won 9–0 on aggregate.----Helsingborg won 5–0 on aggregate.----St Johnstone won 3–1 on aggregate.----Inter Bratislava won 5–1 on aggregate.----Bodø/Glimt won 3–1 on aggregate.----Viking won 18–0 on aggregate.----Maccabi Tel Aviv won 4–3 on aggregate.----Steaua București won 7–1 on aggregate.----Lyngby won 7–0 on aggregate.----Ankaragücü won 2–0 on aggregate.----Zürich won 4–0 on aggregate.----Grasshopper won 8–0 on aggregate.----IFK Göteborg won 3–1 on aggregate.----Dinamo București won 13–2 on aggregate.----Legia Warsaw won 9–0 on aggregate.----Levski Sofia won 2–0 on aggregate.----Anderlecht won 9–1 on aggregate.----3–3 on aggregate. Olimpija Ljubljana won on away goals.----Hajduk Split won 6–1 on aggregate.----Celtic won 10–0 on aggregate.----CSKA Sofia won 8–0 on aggregate.----Ferencváros won 4–2 on aggregate.----Kilmarnock won 2–1 on aggregate.