Abstract Background Health systems have an environmental impact of around 4.6% of global emissions, contributing to aggravating the climate crisis. However, the health impact of the carbon emissions originated by health systems is not regularly assessed. We aim to estimate the health burden and associated costs of the carbon footprint of health systems across the European Union (EU). Methods We calculated DALYs and associated costs based on human health damage factors (DALYs/kg-CO2e) by considering four scenarios. Three scenarios for shared socioeconomic pathways (S1 - high growth, S2 - baseline, and S3 - low growth) represented variations of global society, demographics, and economics until 2100. A fourth scenario (S4) considered the current EU’s 55% reduction goal of greenhouse gas emissions. The healthcare sector’s emissions per capita (in CO2-equivalent) in 2019 were extracted from the Lancet Countdown, and population data were retrieved from Eurostat for the same year. Results In the EU, 365,047 DALYs (95%CI: 194,692-535,403) are expected to be caused by health systems’ emissions at baseline (S2). In an S1 scenario, the burden would slightly decrease to 315,374 DALYs (95%CI: 170,355-462,393), whereas a S3 scenario would increase 486,730 DALYs (95%CI: 243,365-681,422). If EU’s carbon goals are met, the burden could be substantially reduced to 164,271 DALYs (95%CI: 87,611-240,931). The monetisation of DALYs can result in costs amounting to 25.6 billion euros. Conclusions CO2 emissions from health systems are expected to significantly impact human health. It is therefore of the utmost importance to ensure that EU climate policies for healthcare buildings are in line with the Paris Agreement. This will require the implementation of climate mitigation programmes within the health sector and a review of clinical practices at the local level. Key messages • The carbon footprint of health systems is estimated to significantly impact health, with high economic burden. • EU climate policies for healthcare buildings and procurement must be aligned with the Paris Agreement.