Hydatidosis is one of the zoonotic diseases with special importance for public health and causing financial problems in developed and developing countries. This infection is the most prevalent disease in the Middle East especially in Iran. In this survey, internal organs of 1,200 sheep and 1,200 goats, including liver, lung, heart, and kidney, were randomly inspected to estimate prevalence rate of hydatidosis and its relationship with season, sex, age, and infected organs. It was found that a total of 335 (27.9 %) of the 1,200 slaughtered goats and a total of 546 (45.5 %) of the 1,200 slaughtered sheep were infected with the hydatid cysts. Prevalence of hydatidosis in females was significantly (p < 0.05) more than males, and the infection rate was significantly (p < 0.05) increased by age. The most infected organs were liver and lung, respectively, and the least infected organs were kidney and heart, respectively. High prevalence of hydatidosis in Iran can be a result of conventional slaughtering of sheep and goats, availability of carcass wastes and offal for scavenging stray dogs and other wild carnivores, and close relation between shepherd dog and these animals. The prevalence rate can be decreased by interrupting Echinococcus granulosus life cycle, stopping illegal slaughtering, and increasing public awareness about the infection. © 2012 Springer-Verlag London.