Abstract: The emergence of fruit rot diseases and increasing damages in the orchards and storages, lack of data on their causes and control possibilities are among the main concerns of the pome fruit growers. Several pathogenic fungi are known to cause cankers on the trees in orchards and also fruit rots in orchards and storages (e. g. Neofabraea spp., Monilinia spp.). The knowledge on these diseases is still not sufficient, and their significance in many areas is not known. The aim of the present study was to elucidate ability of various fungi isolated from tree cankers of apple and pear to cause fruit rots in the storage. Four apple and four pear cultivars differing in tolerance to fruit rots were used for the studies. Pathogenicity on fruits was characterised for 20 fungal isolates belonging to Neofabraea spp., Fusarium spp., Diaporthe spp., and Valsa spp. in several storage experiments. The differences in ability to cause fruit rot were observed among isolates belonging to the same species and among the species. Eight of thirteen tested isolates originating from tree cankers were also able to cause fruit rot. Neofabraea strains and one Fusarium sp. isolate were most aggressive, and they caused significant damages on most of the tested cultivars. The more aggressive and virulent (degree of damages and ability to infect more cultivars) were Neofabraea spp. and isolates originating from tree cankers.