The management of livestock manure has become increasingly important. Farms are separating, digesting and/or composting to create a value-added product that can either be used on site or sold off-farm. Regardless of the use, disinfection of this animal waste is important to the health of animals and humans. The high temperatures of composting have been shown to inactivate enteric pathogen indicator species such as E. coli but questions remain as to its ability to inactivate hardier pathogens such as Mycobacterium avium paratuberculosis (MAP). MAP, the causal agent of Johne’s disease, is associated with economic losses worldwide. The disease is transmitted among livestock by the fecal-oral route, thus application of contaminated manure, slurry or compost to grazing or cropland could contribute to the spread of the disease. Manure from a Johne’s free farm was mixed with manure from a heavily shedding cow and formed into a windrow. The windrow was turned weekly and temperatures reached > 55oC for the course of the study. Thermophilic composting rendered MAP un-culturable as early as 5 days into the composting process and it remained un-culturable through day 70.