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Intensive farm animal production (IFAP) is being increasingly implemented to meet the rising demand for animal source foods in South Asia. The siting of IFAP facilities in urban or peri-urban areas leads to large proximate animal populations, increasing human exposure to pollutants and pathogens. Improperly managed wastes from IFAP facilities and abattoirs can contaminate water with excess nutrients, pathogens, veterinary pharmaceuticals, antibiotics, heavy metals, and hormones, and can release ammonia, hydrogen sulfide, volatile organic compounds, bioaerosols, and particulate matter into the air compartment. The unregulated nature of IFAP in South Asia creates a risk for zoonotic transmission, including anthrax, brucellosis, Campylobacter, Cryptosporidium, cysticercosis, E. coli, Giardia, Highly Pathogenic Avian Influenza, leptospirosis, Salmonella and Nipah Virus. Recommendations to mediate adverse human health consequences include improved veterinary care, prohibition of confinement facilities that facilitate pathogen transmission and evolution, prohibition of nontherapeutic use of antibiotics, implementation of proper management of animal wastes, zoning for IFAP and abattoir facilities, and surveillance of slaughtering facilities to limit carcass contamination and reduce the burden of foodborne disease in South Asia.