Cystic echinococcosis is endemic and hyperendemic in Uruguay. The objective of this study was to determine the species and genotype of Echinococcus granulosus sensu lato in symptomatic patients with cystic echinococcosis who underwent surgery, together with the location and stage of the cysts. The study included 13 patients aged between 6 and 57 years old. Samples of cysts from these cases were analyzed using DNA extraction, polymerase chain reaction amplification and sequencing. The results revealed the presence of E. granulosus sensu stricto in all cases, with 12 samples belonging to the G1 genotype and 1 to the G3 genotype, suggesting that disease persistence might be related to the dog–sheep cycle. However, other intermediate hosts, such as cattle, could also be involved. Cysts were most frequently found in the liver, followed by muscle and other sites (e.g. pulmonary, vertebral, pelvic and cardiac); and stage CE1 was most frequently found, followed by CE2 and CE3b. Three cases occurred in children or adolescents, suggesting an active parasite cycle in at least some areas of the country. Since there is considerable diversity of E. granulosus sensu lato species and genotypes in South America, it is important to continue the present study in order to draw stronger epidemiological conclusions.