The third round of the 1999–2000 UEFA Cup began on 23 November 1999. The round included 24 winners from the second round as well as 8 third placed teams from the Champions League First group stage.
Second leg
Juventus won 4–3 on aggregate.
Borussia Dortmund 2–2 Rangers on aggregate. Borussia Dortmund won 3–1 on penalties.
Werder Bremen won 4–3 on aggregate.
Leeds United 2–2 Spartak Moscow on aggregate. Leeds United won on away goals rule.
Celta Vigo won 8–1 on aggregate.
Roma won 1–0 on aggregate.
Deportivo La Coruña won 5–3 on aggregate.
Arsenal won 6–3 on aggregate.
Mallorca won 3–0 on aggregate.
AS Monaco won 3–2 on aggregate.
Lens won 5–3 on aggregate.
Parma won 5–4 on aggregate.
Slavia Prague won 5–2 on aggregate.
Atlético Madrid won 5–3 on aggregate.
Galatasaray won 3–2 on aggregate.
Bayer Leverkusen 2–2 Udinese on aggregate. Udinese won on away goals rule.