We investigated the availability of health system performance indicator data in Canada's 18 northern regions and the feasibility of using the performance framework developed by the Canadian Institute for Health Information [CIHI]. We examined the variation in 24 indicators across regions and factors that might explain such variation. The 18 regions vary in population size and various measures of socioeconomic status, health-care delivery, and health status. The worst performing health systems generally include Nunavut and the northern regions of Québec, Manitoba and Saskatchewan where indigenous people constitute the overwhelming majority of the population, ranging from 70% to 90%, and where they also fare worst in terms of adverse social determinants. All northern regions perform worse than Canada nationally in hospitalisations for ambulatory care sensitive conditions and potentially avoidable mortality. Population size, socioeconomic status, degree of urbanisation and proportion of Aboriginal people in the population are all associated with performance. The North is far from homogenous. Inter-regional variation demands further investigation. The more intermediate pathways, especially between health system inputs, outputs and outcomes, are largely unexplored. Improvement of health system performance for northern and remote regions will require the engagement of indigenous leadership, communities and patient representatives.