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Anaerobic digesters are becoming a popular waste treatment option in New York State. These systems generate energy for on-farm use and sale while providing significant odor reduction. Research has shown that mesophilic systems (T=100oF) have the potential to reduce pathogens entering the environment. A plug flow digester was monitored for 14 months starting in May 2001. Samples taken from the digester influent and effluent were tested for the fecal coliform group of indicator organisms and Mycobacterium avium subspecies paratuberculosis (Map). M. avium paratuberculosis is the microorganism responsible for Johnes disease in dairy cattle and other ruminants. Results show almost a 3-log reduction in fecal coliforms and slightly more than a 2-log reduction in Map. This paper describes an anaerobic digester and shows the comparative results of testing between a farm with a digester and a farm without a digester. Since both farms in this study compost and sell excess solids, analyses were done on the composted manure as well.