BACKGROUND: Previous research has identified the role of social capital in explaining variations in health in the countries of the former Soviet Union. This study explores whether the benefits of social capital vary among these countries and why. METHODS: The impact of micro social capital (trust, membership and social isolation) on individual health was estimated in each of eight former Soviet republics using instrumental variables to overcome methodological hazards such as endogeneity and reverse causality. Interactions with institutional variables (voice and accountability, effectiveness of the legal system, informal economy) and social protection variables (employment protection, old age and disability benefits, sickness and health benefits) were examined. RESULTS: Most social capital indicators, in most countries, are associated with better health but the magnitude and significance of the impact differ between countries. Some of this variation can be explained by interacting social capital indicators with measures of institutional quality, with membership of organisations bringing greater benefit for health in countries where civil liberties are stronger, whereas social isolation has more adverse consequences where there is a large informal economy. A lesser amount is explained by the interaction of social capital indicators with selected measures of social protection. CONCLUSION: When considering interventions to improve social capital as a means of improving population health, it seems advisable to take into account the influence of macrocontextual variables, in order not to overstate or understate the likely impact of the intervention.