Israel is a high-income country with an advanced health system and universal health-care insurance. Overall, the health status has improved steadily over recent decades. We examined differences in morbidity, mortality, and risk factors for selected non-communicable diseases (NCDs) between subpopulation groups. Between 1975 and 2014, life expectancy in Israel steadily increased and is currently above the average life expectancy for the Organisation for Economic Co-operation and Development countries. Nevertheless, life expectancy has remained lower among Israeli Arabs than Israeli Jews, and this gap has recently widened. Age-adjusted mortality as a result of heart disease, stroke, or diabetes remains higher in Arabs, whereas age-adjusted incidence and mortality of cancer were higher among Jews. The prevalence of obesity and low physical activity in Israel is considerably higher among Arabs than Jews. Smoking prevalence is highest for Arab men and lowest for Arab women. Health inequalities are also evident by the indicators of socioeconomic position and in subpopulations, such as immigrants from the former Soviet Union, ultra-Orthodox Jews, and Bedouin Arabs. Despite universal health coverage and substantial improvements in the overall health of the Israeli population, substantial inequalities in NCDs persist. These differences might be explained, at least in part, by gaps in social determinants of health. The Ministry of Health has developed comprehensive programmes to reduce these inequalities between the major population groups. Sustained coordinated multisectoral efforts are needed to achieve a greater impact and to address other social inequalities.