Background Cystic echinococcosis (CE) is a zoonosis caused by the cestodes of the Echinococcus species. Its life cycle involves dogs and other canids as definitive hosts for the intestinal tapeworm, as well as domestic and wild ungulates as intermediate hosts for the tissue-invading metacestode (larval) stage. The disease has a special impact on disadvantaged pastoralist communities and is listed now among the three top priority neglected tropical disease (NTD).Therefore, CE is a neglected disease even in high endemicity regions. This study aimed at investigation of the prevalence of CE in different animals slaughtered for food consumption in Sinnar area, Blue Nile states in Sudan.Methods A survey of CE in livestock was conducted from April 2009 to March 2011 in Sinnar area, Blue Nile state in Sudan. Location, parasitological status and fertility conditions were determined. In addition, 120 hydatid cysts (30 from camels, 62 from cattle and 28 from sheep) were examined by polymerase chain reaction (PCR) and mitochondrial gene sequencing for the genetic allocation of Echinococcus strains or species Results The prevalence of CE was 29.7％ (30/101) in camels, 2.7％ (62/2310) in cattle and 0.6％ (26/4378) in sheep. It was shown that infection rates increased with age in camels, cattle and sheep. In camels, 67％ (20/30) of the infected animals were aged between 2-5 years whereas 58％ (36/62) of the infected cattle were ＞5 years. In sheep, the prevalence rate was distributed equally between animals ranging 2-5 years and ＞5 years. Even though multiple cysts were found in some animals, the average number of cysts per animal was close to 1 in all examined species. Lungs were found to be the predilection sites for the parasite in both camels and cattle, while most of the cysts found in sheep were located in the liver. About 63.4％ of cysts encountered in camels were considered as large (5-7 cm), whereas those in cattle and sheep were medium (2-4 cm) and small (＜2 cm) respectively. The highest fertility rate was found in camel cysts with 85.4％ (35/41) followed by cattle (50.0％, 32/64) and sheep (39.0％, 11/28). All examined cysts belonged to Echinococcus canadensis G6, which was confirmed to be the overwhelmingly predominant species in that area.Conclusion The epidemiological situation in Sinnar area, Blue Nile state is characterized by intense transmission of Echinococcus canadensis G6, thereby closely resembling the situation in most other regions of Sudan.