A veterinary research project is organized in Danish biogas plants (BGP) to study the ‘pathogen reducing effect’ (PRE) of the treatment in digestion tanks and sanitation tanks, and the ‘pathogen reducing capacity’ (PRC) of the entire plant. In addition the feasibility of measures to prevent spread of animal and human pathogens is studied. Ten BGPs are currently in operation closely related to the agricultural sector. Slurry constitutes 80-85% of the biomass treated, various industrial by-products and urban waste the rest. Rules have been issued to prevent spread of pathogens between animal holdings during the collection, transport and distribution of biomass. Criteria for the treatment in digestion tanks and sanitation tanks have been introduced to ensure removal of pathogens. Official regulations on hygienic measures and conditions for treatment of biomass which is spread on agricultural land are included in Danish legislation. An indicator method based on faecal enterococci (streptococci) (FE) has proven its practical value for checking the functions, detecting leakage or wrong management, and for evaluating the PRE at temperatures below 55 to 60°C. Studies of the persistence of pathogens in biomass at higher temperatures are in progress. The role of the competent central, regional and local authorities for approval, regular supervision and inspection of the BGPs is described. The Veterinary Service takes action when outbreaks of serious diseases occur.