Abstract Background Vaccine hesitancy threatens public health. Some evidence suggests that vaccine hesitancy in Europe may be linked with the success of populist parties, but more systematic analysis is needed. Methods We examine the prevalence of individual-level vaccine hesitancy across the European Union (EU) and its association with political orientations. We also analyze whether success of populist parties is linked with vaccine hesitancy and uptake. We draw on individual-level Eurobarometer data from 2019, with a total of 27 524 respondents across the EU. We also rely on national and regional-level populist party vote shares. Finally, for a time-series analysis, we rely on aggregated populist party support as measured in the European Social Survey waves 1–9 (2002–18), and national immunization coverage rates from the WHO from 2002 to 2018. Results While vaccine hesitancy is confined to a minority of the population, this group is large enough to risk herd immunity. Political orientations on a left-right dimension are not strongly linked to vaccine hesitancy. Instead, vaccine hesitancy is associated with anti-elite world views and culturally closed rather than cosmopolitan positions. Conclusions Vaccine hesitancy is not only present in all EU member states but also maps on broader dimensions of cultural conflict. Hesitancy is rooted in a broader worldview, rather than misperceptions about health risks. Pro-vaccine interventions need to consider the underlying worldview, rather than simply targeting misperceptions.