The aim of our study was to monitor and analyze the main biological hazards connected to the long-term storage of wood chips for energy production. The analysis was carried out in four high-capacity storage yards of the town heating plants in the Banská Bystrica self-governing region in Slovakia. Five samples were taken from each pile of a rectangular shape and volume over 4,000 m³; the sampling was carried out at the beginning of the monitoring period and at the end of the monitoring period (after one year). Thirtyfour species of microscopic fungi were identified (18 at the beginning of the monitoring period and 16 at the end of the monitoring period). Thirty-three of them can potentially cause severe diseases. Fungi of the genus Aspergillus, causing severe diseases, were identified as the most abundant. The research confirmed that if the length of storage time is more than a year, the potential hazards for human health increase due to the increasing number of spore-forming pathogens. Following the monitoring of atmospheric conditions the highest increase of harmful spores was recorded at the average annual temperature of 10ºC and precipitation of over 1,000 mm a year.