The quantitative resistance of sugar beet (Beta vulgaris L.) against Cercospora leaf spot (CLS) caused by Cercospora beticola (Sacc.) was characterised by hyperspectral imaging. Two closely related inbred lines, differing in two quantitative trait loci (QTL), which made a difference in disease severity of 1.1-1.7 on the standard scoring scale (1-9), were investigated under controlled conditions. The temporal and spatial development of CLS lesions on the two genotypes were monitored using a hyperspectral microscope. The lesion development on the QTL-carrying, resistant genotype was characterised by a fast and abrupt change in spectral reflectance, whereas it was slower and ultimately more severe on the genotype lacking the QTL. An efficient approach for clustering of hyperspectral signatures was adapted in order to reveal resistance characteristics automatically. The presented method allowed a fast and reliable differentiation of CLS dynamics and lesion composition providing a promising tool to improve resistance breeding by objective and precise plant phenotyping.