Nagaland is a state in the north-east India with around 2 million inhabitants. Pork occupies an important place in the diet of Naga. Most people buy and sell pork in informal markets (called wet markets) where there is little safety and quality regulation. As part of a larger project on competitiveness of smallholder pig production in Nagaland, we carried out a comparative risk assessment to identify and characterise hazards present in representative pork meat chains. The study addressed all levels (“from stable to table”) of rural pork supply chains as well as peri-urban and rural food supply chains supplying Guwahati, the state capital. We used Participatory Risk Analysis, a new method for assessing and managing food-safety that allows rapid and participatory assessment of hazards in resource-constrained environments. Different tools were applied including the following: 1) Participatory rural appraisal to understand pigs farming systems and disease problems; 2) Individual questionnaires for value chain actors and consumers; 3) Observational check-lists covering practices at slaughter, transport and retail; 4) Standard microbiological tests for total bacterial contamination and faecal bacteria; and 5) Rapid diagnostic tests for several pathogens in pork meat, including several bacteria, different parasites and antibiotic residues. The collected data were evaluated to assess hazards as well as risk amplifying or mitigating practices. We found high levels of important food-borne hazards, many reported for the first time in Nagaland. Hygienic practices at slaughter and retail are very poor and there is a high risk of cross-contamination at the household level. Although some risk-mitigating practices are evident (in particular lengthy cooking of meat) other risk enhancing practices exist (such as smoking pork in the household fires and eating without cooking). The study identifies critical control points and makes evidence-based recommendations for better managing porkborne illness in Nagaland.