Composting has been used to dispose of animal mortalities and infected materials, such as manure and feed, during major animal disease outbreaks. In this study, we adapted the plastic-wrapped mortality composting system developed by the Canadian Food Inspection Agency during the 2004 highly pathogenic avian influenza outbreak to compost swine mortalities. The goals of the study were to evaluate the performance of the plastic-wrapped composting system to dispose of swine mortalities and to field test its ability to eliminate the spread of airborne pathogens through the aeration ducts. Two cover materials, ground cornstalks and woodchips, were tested using passively and actively aerated composting sheds. The mortalities were inoculated with Salmonella spp. and vaccine strains of Bovine herpesvirus-1 and Bovine viral diarrhea virus. Air samples collected from the upper aeration duct (air outlet) during the first 10 d of composting were negative for Salmonella and the viruses tested, which indicated that aerosol transmission of the pathogens was limited. The aeration plenum placed under the mortalities helped to keep conditions aerobic, as O2 concentrations of both passively and actively aerated test units were above 11%. Actively aerated cornstalks had the highest degree-hours (1,462 °C h d−1), which was followed by passively aerated cornstalks (1,312 °C h d−1), actively aerated woodchips (1,303 °C h d−1), and passively aerated woodchips (1,062 °C h d−1). After a 7-wk composting period, all three pathogens were inactivated based on quantitative polymerase chain reaction test results. The mortalities were not inoculated with the African swine fever virus, but temperature data showed that if they were, the system had the potential to eliminate this virus.