Introduction: The exact prevalence of polycystic ovary syndrome (PCOS) is difficult to assess due to the clinical heterogeneity of this condition, the lack of a universal definition as well as the lack of studies comparing differences within and between ethnic groups across geographical regions. Material and methods: Using a modeling approach, we analyzed the data from Global Burden of Disease Study 2016 and extracted the national and regional estimates on PCOS prevalence since 1990 in females aged 15-49 years by country and three major European regions: Western, Central, and Eastern. Results: The average prevalence of PCOS in Europe was 276.4 cases per 100,000 (95% uncertainty interval (UI): 207.8-363.2). The estimates varied markedly across countries and regions, with the highest rates per 100,000 in the Czech Republic (460.6) and the lowest in Sweden (34.10); other Nordic countries, Germany, and the UK had relatively low rates as well. The rates in Central and Eastern Europe were more than three times higher than those in Western countries. They were comparable among Eastern countries, ranging from 406.4 in Lithuania to 443.1 in Russia. Within Central Europe, PCOS prevalence was lowest in Turkey and Albania, while in the majority of the remaining countries, the prevalence ranged between 420 and 440 per 100,000. Between 1990 and 2016, the rates across European regions were relatively stable. Conclusions: We found highly variable national and regional prevalence of PCOS among European females. Our estimates encourage the search at the population level for new environmental and genetic determinants of PCOS.