Poor sanitation and insufficient disposal of sewage and faeces are primarily responsible for water associated health problems in developing countries. Domestic sewage and faeces are prevalently discharged into surface waters which are used by the inhabitants as a source for drinking water. This paper presents a decentralized anaerobic process technique for handling of such domestic organic waste. Such an efficient and compact system for treating faeces and food waste may be of great benefit for developing countries. Besides a stable biogas production for energy generation, the reduction of bacterial pathogens is of particular importance. In our research we investigated the removal capacity of the reactor concerning pathogens, which has been operated under thermophilic conditions. Faecal coliforms and intestinal enterococci have been detected as indicator organisms for bacterial pathogens. By the multiple regression analysis technique an empirical mathematical model has been developed. The model shows a high correlation between removal efficiency and both, hydraulic retention time (HRT) and temperature. By this model an optimized HRT for defined bacterial pathogens effluent standards can be easily calculated. Thus, hygiene potential can be evaluated along with economic aspects. In this paper not only results for describing the hygiene potential of a thermophilic anaerobic bioreactor are presented, but also an exemplary method to draw the right conclusions out of biological tests with the aid of mathematical tools.