The qualifying round matches of the 1999–2000 UEFA Cup were played on 12 and 26 August 2000.
The following 76 teams participated in the qualifying round.
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.
Kryvbas Kryvyi Rih won 5–0 on aggregate.
Maccabi Tel Aviv won 4–3 on aggregate.
3–3 on aggregate; Olimpija Ljubljana won on away goals.