For the years 2012–2018, we investigated the occurrence of storage diseases caused by fungi on four cultivars of apples grown in the central part of Poland. The fruits were picked in orchards managed with Integrated Pest Management (IPM) practices and stored in a cold room for 5–7 months. Depending on the season, apple cultivar and localization of orchard, the incidence of diseases was different. On apple cvs “Gala”, “Ligol” and “Golden Delicious”, bull’s eye rot (Neofabraea spp.) was the most frequently observed disease, whereas on apple cv. “Gloster”, gray mold (Botrytis cinerea) predominated. The blue mold (Penicillium expansum), brown rot (Monilinia spp.) and fungi of Alternaria spp. occurred at significantly lower intensity. We detected the occurrence of the new storage diseases of apples caused by Colletotrichum spp., Neonectria ditissima and Diaporthe eres.