Risk-based inspection provides a framework whereby inspection resources can be prioritized and targeted towards foods that pose the highest risk to human health. To provide a risk assessment of the initial biological hazards associated with foods consumed, criteria related to hazard identification, hazard characterization and exposure assessment were developed for all foods inspected by the Canadian Food Inspection Agency.Using Canadian scientific data, food-pathogen pairs most responsible for foodborne illness were developed and ranked. To characterize the overall population burden of these food-pathogen pairs, a model adapted from the European Food Safety Authority (EFSA) was developed which incorporated criteria related to pathogen characteristics and probability of exposure of humans by food.The top risk-ranked food-pathogen pairs were Campylobacter spp. and poultry, pathogenic Escherichia coli and beef, Salmonella spp. and poultry, Salmonella spp. and produce, and Campylobacter spp. and dairy.