The Echinococcus granulosus tapeworm is responsible for cystic echinococcosis (CE), a zoonotic disease with worldwide distribution. The life cycle of the parasite is mainly domestic and takes place between dogs and livestock species. A slaughterhouse survey was conducted in 2012 in the Republic of Moldova in order to estimate the prevalence of CE. A total of 1525 cattle, 5580 sheep and 12,700 pigs were surveyed. No CE infection was observed in pigs, while prevalence was estimated at 59.3% in cattle and 61.9% in sheep. Infection was significantly higher in animals raised in private households than in those from collective farms. The frequency of infection increased with age in both species. In cattle and in sheep, infection of both the liver and lungs was the most common, while infection in the lungs only was much less frequent. Farm type appears to be an important factor in CE infection in Moldova, due to the extensive farming and the home-slaughtering undertaken in the majority private sector, despite a high prevalence of CE also recorded in the public sector. The low fertility of cysts in cattle (1.1%) compared to sheep (47.6%) confirmed the maintenance of E. granulosus sensu stricto in a dog-sheep life cycle which excludes cattle. Further studies are needed to obtain a complete overview of the parasite's epidemiology in its intermediate and definitive hosts, in order to implement control and preventive measures, with specific attention given to farms in the private sector.