Background In order to support the case for inter-sectoral policies to tackle health inequalities, the authors explored the economic costs of socioeconomic inequalities in health in the European Union (EU). Methods Using recent data on inequalities in self-assessed health and mortality covering most of the EU, health losses due to socioeconomic inequalities in health were calculated by applying a counterfactual scenario in which the health of those with lower secondary education or lower (roughly 50% of the population) would be improved to the average level of health of those with at least higher secondary education. We then calculated various economic effects of those health losses: healthcare costs, costs of social security schemes, losses to Gross Domestic Product (GDP) through reduced labour productivity and the monetary value of total losses in welfare. Results Inequality related losses to health amount to more than 700 000 deaths per year and 33 million prevalent cases of ill health in the EU as a whole. These losses account for 20% of the total costs of healthcare and 15% of the total costs of social security benefits. Inequality related losses to health reduce labour productivity and take 1.4% off GDP each year. The monetary value of health inequality related welfare losses is estimated to be (sic)980 billion per year or 9.4% of GDP. Conclusion Our results suggest that the economic costs of socioeconomic inequalities in health in Europe are substantial. As this is a first attempt at quantifying the economic implications of health inequalities, the estimates are surrounded by considerable uncertainty and further research is needed to reduce this. If our results are confirmed in further studies, the economic implications of health inequalities warrant significant investments in policies and interventions to reduce them.