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Governments are increasingly looking to vaccination to provide a path out of the COVID-19 pandemic. Hungary offers an example to investigate whether social inequalities compromise what a successful vaccine program can achieve. COVID-19 morbidity, mortality, and vaccination coverage were characterized by calculation of indirectly standardized ratios in the Hungarian population during the third pandemic wave at the level of municipalities, classified into deprivation quintiles. Then, their association with socioeconomic deprivation was assessed using ecological regression. Compared to the national average, people living in the most deprived municipalities had a 15–24% lower relative incidence of confirmed COVID-19 cases, but a 17–37% higher relative mortality and a 38% lower vaccination coverage. At an ecological level, COVID-19 mortality showed a strong positive association with deprivation and an inverse association with vaccination coverage (RRVaccination = 0.86 (0.75–0.98)), but the latter became non-significant after adjustment for deprivation (RRVaccination = 0.95 (0.84–1.09), RRDeprivation = 1.10 (1.07–1.14)). Even what is widely viewed as one of the more successful vaccine roll outs was unable to close the gap in COVID-19 mortality during the third pandemic wave in Hungary. This is likely to be due to the challenges of reaching those living in the most deprived municipalities who experienced the highest mortality rates during the third wave. [ABSTRACT FROM AUTHOR]