Cystic echinococcosis (CE) remains a significant challenge in Uganda with precise status largely undocumented in most communities. To determine CE prevalence, post-mortem examination was done on 14 937 livestock (5873 goats, 1377 sheep, 3726 zebu cattle and 3054 Ankole cattle) slaughtered in abattoirs in the districts of Moroto in Karamoja region, Kumi in Teso region and Nakasongola and Luwero in Buganda region. The overall CE prevalence was 21.9% in sheep, 15.2% in zebu cattle, 5.5% in goats and 2.1% in Ankole cattle. Moroto district had a higher prevalence of CE than other districts with 31.3% in zebu cattle, sheep 28%, goats 29.1% and (0%) in Ankole cattle. On organ locations, the lungs were the most affected in all livestock in all the study areas. Considering cyst fertility, 33.9, 1.7 and 6.4% of Ankole cattle, sheep and zebu cattle respectively had fertile cysts in the liver while 4.5% of goats and 4% Ankole cattle had fertile cysts in the lungs. In conclusion, CE is widespread and occurs among cattle, sheep and goats in pastoral and agro-pastoral areas in Uganda. Therefore, there is an urgent need to create awareness among the communities on role of livestock in CE epidemiology and transmission.