A cross-sectional study was conducted at Gumbo slaughter slab in Juba, Central Equatoria State (CES) in South Sudan, between October and December 2015, to determine the prevalence of cystic echinococcosis (CE) and to estimate the direct economic losses associated with condemnation of infected organs in slaughtered goats. A thorough postmortem examination was conducted on carcasses of a total of 1126 goats selected by systematic random sampling for detection of CE in the lungs, liver, heart,

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... eys, and the spleen. Moreover, CE-related direct financial losses were estimated by using a standardized formula. The overall prevalence of CE was found to be 281 (24.9%, 95% CI 22.5–27.6). Furthermore, old age (OR = 2.61, p value < 0.001), Mubende breed (OR = 2.97, p value < 0.001), and Ugandan geographical origin (OR = 2.97, p value < 0.001) were associated with higher prevalence of CE. The lungs were the most affected organ with a prevalence of 55.2% followed by liver (44.1%), and the spleen (0.07%). A direct CE-related monetary loss of 78.820 South Sudanese Pounds (SSP) per year was estimated. This loss is equivalent to USD 43.788. In conclusion, CE is considerably prevalent and is associated with significant direct financial losses among goats slaughtered at Gumbo slaughter slab in Juba, CES, South Sudan.