Abstract Background and AimsBunch rot symptoms can appear weeks after the infection of grape flowers by Botrytis cinerea. Quantitative polymerase chain reaction (qPCR) detects changes in the DNA mass of a target organism and is a potential tool for studying quiescent infections. The aim was to optimise a duplex qPCR to quantify B. cinerea DNA in the background of endogenous Vitis vinifera DNA. Methods and ResultsThree DNA extraction techniques and three probe sets were compared. The optimised qPCR using the Bc3 probe set was 1000-fold more sensitive than other probe sets, with a threshold cycle value of.