The draw for this round was performed on 30 June 1999 in
Geneva,
Switzerland. Unlike the future seasons of Champions League qualification, all winners of previous round were treated as unseeded regardless of their coefficients.
Seeding ;Notes
Summary Matches Rapid Wien won 5–0 on aggregate. ----
Anorthosis Famagusta won 3–2 on aggregate. ----
Partizan won 6–1 on aggregate. ----
Molde won 4–2 on aggregate. ----
5–5 on aggregate; Widzew Łódź won 3–2 on penalties. ----
Rangers won 7–1 on aggregate. ----
Zimbru Chișinău won 3–2 on aggregate. ----
AIK won 3–0 on aggregate. ----
Brøndby won 2–0 on aggregate. ----
Skonto won 5–4 on aggregate. ----
1–1 on aggregate; Hapoel Haifa won on away goals. ----
Dynamo Kyiv won 3–0 on aggregate. ----
MTK Hungária won 5–1 on aggregate. ----
Maribor won 5–4 on aggregate. ==Third qualifying round==