The qualifying rounds for the 1999–2000 UEFA Champions League began on 13 July 1999.
In total, there were three qualifying rounds which provided 16 clubs to join the group stage.
Partizan Skonto Zimbru Chișinău Litex Lovech Haka Žalgiris
Sloga Jugomagnat Barry Town Flora Tsement Ararat Glentoran St Patrick's Athletic Valletta
Unlike the future seasons of Champions League qualification, all winners of previous round were treated as unseeded regardless of their coefficients.
[1] Dynamo Kyiv Brøndby Rapid Wien Beşiktaş Rangers
CSKA Moscow Widzew Łódź Rapid București Dinamo Tbilisi Genk Slovan Bratislava MTK Hungária Rijeka Molde Anorthosis Famagusta Maribor Hapoel Haifa Dnepr-Transmash Mogilev Partizan[†] Skonto[†] Zimbru Chișinău[†] Litex Lovech[†] Haka[†] Žalgiris[†]
Unlike the future seasons of Champions League qualification, all winners of previous round were treated as unseeded regardless of their coefficients.
[1] Parma Borussia Dortmund Spartak Moscow Chelsea PSV Eindhoven Lyon Fiorentina Valencia Mallorca AEK Athens Galatasaray Croatia Zagreb Hertha BSC Boavista Sturm Graz AaB Servette Teplice Dynamo Kyiv[†] Brøndby[†] Rapid Wien[†] Hapoel Haifa[†] Rangers[†]
Molde[†] Widzew Łódź[†] Skonto[†] Zimbru Chișinău[†] Maribor[†] Anorthosis Famagusta[†] MTK Hungária[†] Partizan[†] The losing teams advanced to the first round of the 1999–2000 UEFA Cup.