Biogas stations are currently an important part of agricultural production management. They can be fed besides other things with bio-waste materials to produce biogas and heat. While corn and grass silages are the main feedstock for anaerobic digestion in agricultural biogas plants, to a lesser extent, cattle, swine or poultry manure are often used. This, however, poses certain health risks. The problem may be an increased incidence of bacterial pathogens that are commonly related to animal husbandry. The aim of the study was to compare different types of manure with regard to the content of selected zoonotic agents and to monitor the extent of their elimination by an anaerobic digestion process in biogas fermenters.