Apple fruit rot can be caused by several fungi. In Northern Europe, the most common storage rot, Bull’s eye rot, is caused by Neofabraea spp., bitter rot by Colletotrichum spp., brown rot by Monilinia fructigena, grey mould is caused by Botrytis cinerea and Fusarium rot by several Fusarium species. Blue mold decay caused by Penicillium expansum is an important disease in several European countries. Incidence of different causal agents may vary depending on cultivar, climate during growing season and agricultural practices. The main objective of the study was to obtain baseline information about apple rot-causing fungi, their incidence during fruit storage and to evaluate the fungicide sensitivity of most of isolated fungal species. The study was performed during the storage period of apples after the growth season of 2013. Rotten apples were sorted in the storage and part of them was brought to the laboratory in order to obtain fungal isolates. Fungi were identified according to the morphological characteristics and sequencing of the ITS1-5.8S-ITS2 region. During storage in February and March the total percentage of rotten apples in various cultivars varied from 3.6 to 58.9%. All post-harvest diseases described in Northern Europe were detected. In part of the storehouses apple rot caused by Cadophora luteo-olivacea was observed. Alternaria spp. and Cladosporium spp. were detected on few apples as secondary infection agents. Using the most often isolated fungal species, sensitivity tests were performed against five commonly used fungicides. In general, the sensitivity of tested fungi to the fungicides was high with exception of several Neofabraea and Alternaria isolates.