Introduction On-farm anaerobic digestion (AD) which has expanded in Europe, produced biogas and a by-product (digestate) used as fertilizer. However, very few studies have been devoted to the effect of AD on the level of pathogenic bacteria. The study aims to evaluate the impact of mesophilic AD on the concentrations of zoonotic pathogenic bacteria (Listeria monocytogenes, Salmonella spp, thermotolerant campylobacters) and on indicator bacteria (E. coli and enterococci) in manures and in raw digestates sampled in three biogas plants (BGP). Materials and Methods Samples were collected in storage tank (manures) and at the outlet valve of the digester (raw digestates) from three BGP during a one-year period (8 sampling dates per BGP, 3 replicates per sampling date). Two digesters were fed with pig manure. The third digester was essentially fed with cattle manure. Indicator bacteria were enumerated on specific agar media. Pathogenic bacteria were quantified after an enrichment step by MPN. A total of 144 samples (72 inputs, 72 digestates) were analyzed. Results The pathogens have been detected in manure at a frequency ranged between 92 and 96%. They were also present in raw digestate at a frequency of 38% (thermotolerant campylobacters), 83% (L. monocytogenes) and 88 % (Salmonella spp.). The concentrations were lower in raw digestates than in manures. The average concentrations of thermotolerant campylobacters, L. monocytogenes and Salmonella spp. in raw digestates were 2, 23 and 5 MPN/g, respectively. The average levels of E.coli and enterococci (104-105 cfu/g in manure) decreased by 1 to 2 Log10 during AD. Conclusion Although mesophilic AD did not eliminate the pathogenic bacteria, it reduced their concentration. Raw digestates are not directly spread on agricultural land. It is thus likely that their post-treatment (eg. storage or post-digestion) also contribute to limit the spread of pathogens together with the digestate onto agricultural land.