Few studies have addressed the effect of gender policies on women's health and gender inequalities in health. This study aims to analyse the relationship between the orientation of public gender equality policies and gender inequalities in health in European countries, and whether this relationship is mediated by gender equality at country level or by other individual social determinants of health. A multilevel cross-sectional study was performed using individual-level data extracted from the European Social Survey 2010. The study sample consisted of 23,782 men and 28,655 women from 26 European countries. The dependent variable was self-perceived health. Individual independent variables were gender, age, immigrant status, educational level, partner status and employment status. The main contextual independent variable was a modification of Korpi's typology of family policy models (Dual-earner, Traditional-Central, Traditional-Southern, Market-oriented and Contradictory). Other contextual variables were the Gender Empowerment Measure (GEM), to measure country-level gender equality, and the Gross Domestic Product (GDP). For each country and country typology the prevalence of fair/poor health by gender was calculated and prevalence ratios (PR, women compared to men) and 95% confidence intervals (CI) were computed. Multilevel robust Poisson regression models were fitted. Women had poorer self-perceived health than men in countries with traditional family policies (PR = 1.13, 95%CI: 1.07-1.21 in Traditional-Central and PR = 1.27, 95%CI: 1.19-1.35 in Traditional-Southern) and in Contradictory countries (PR = 1.08, 95%CI: 1.05-1.11). In multilevel models, only gender inequalities in Traditional-Southern countries were significantly higher than those in Dual-earner countries. Gender inequalities in self-perceived health were higher, women reporting worse self-perceived health than men, in countries with family policies that were less oriented to gender equality (especially in the Traditional-Southern country-group). This was partially explained by gender inequalities in the individual social determinants of health but not by GEM or GDP.