Anaerobic digestion is continually gaining importance for the processing of the organic fraction of municipal solid wastes. Although methods for studying the survival of pathogen exist, these methods often need adaptations, are expensive, time consuming or generally not well suited for the harsh conditions within an anaerobic digestion system. In the present study we investigated the applicability of commercially available, mechanically stable and inexpensive pathogen carriers to validate in situ pathogen inhibition within a 750,000l thermophilic, bio-waste treating anaerobic digester. None of the pathogens investigated (Listeria monocytogenes, Salmonella enterica, Escherichia coli, and Campylobacter jejuni) was capable of survival under the conditions of the biogas reactor for more than 24 h indicating that the temperature and physico-chemical properties of the sludge of the fermenter were effective in inhibiting the survival of these microorganisms.