Background Cystic echinococcosis (CE) is a neglected zoonotic infection that is distributed worldwide and prioritised by WHO for control efforts. A big proportion of CE cases do not reach official records, resulting in an underestimate of the magnitude of the public health problem. Indeed, current infection and burden estimates heavily rely on modelling approaches to fill in data gaps, using arbitrary assumptions and highly heterogeneous data sources; as a result, infection and disease burden are likely underestimated. Aim This study aims to estimate the prevalence of abdominal CE, cyst stage distribution and number of infected individuals in the rural population of Bulgaria, Romania, and Turkey. Methods The biggest research-based abdominal US screenings (2014-15) were conducted on 24,693 people in 50 villages (4 districts of Bulgaria, 5 districts of Romania, and 6 provinces of Turkey). Findings Age and sex adjusted prevalence of abdominal CE was: 0.41% in Bulgaria, 0.41% in Romania, 0.59% in Turkey. The estimated number of individuals who may be presently infected with CE in rural areas is around 151,000 (7,872 in Bulgaria, 37,229 in Romania, 106,237 in Turkey). Interpretation Our results provide population-based estimates of the prevalence of abdominal cystic echinococcosis. These findings should be useful to support the planning of cost-effective interventions, supporting the WHO roadmap for cystic echinococcosis control.