In addition to silage, biological waste from cattle, pigs or poultry is also an important input raw material for anaerobic digestion in biogas plants. However, fugate, a waste product from biogas production that is regularly used in agriculture as a fertilizer, may contain bacterial pathogens causing a variety of zoonoses. Anaerobic digestion (AD), the main method of stabilizing biological solids, can effectively and largely inactivate viable pathogens, including parasites, viruses, and pathogens containing antibiotic resistance genes. This review aims to provide a critical overview of the inactivation of biogas plant-related pathogens using AD, which has raised serious concerns about the effectiveness and rationality of AD in controlling pathogens in the plant. Basic deactivation mechanisms and influencing factors were discussed with a focus on modeling related to pathogens and technological aspects of AD. The aim of the study is to compare the diversity of potential bacterial pathogens in different types of slurry, all using molecular-biological methods at the DNA level. Communities were examined by T-RFLP fragment analysis and sequencing of the 16S rRNA. The study aims to raise awareness of the diversity of potential animal pathogens and the impact of anaerobic digestion on the composition of the bacterial community, and overall to help improving the hygiene of agricultural production.