Hydatid cysts are the main cause of human-animal disease transmission, so that we witness substantial economic and health damage due to this every year. Fertile cysts and their protoscoleces viability are important factors for the stability of the parasite cycle and the survival of infection in humans and animals. The aim of this study was to investigate the fertility rate of hydatid cysts and protoscoleces viability in livestock slaughtered in Ilam industrial slaughterhouse. In this study, organs (liver and lung) infected with hydatid cysts in sheep and cows were collected during intermittent periods during June to September 2016 and transferred to the parasitology laboratory of Ilam Veterinary Network. In the laboratory, cysts were first classified based on their type and microscopic characteristics (calcified, purulent, and active). The active cysts were then prepared for the next steps. Of the 175 cysts examined, 86 were obtained from cows and 89 from sheep. Of these, 94 cysts were diagnosed as hepatic and 81 as pulmonary. Average viability of fertile cyst protoscoleces was obtained (73.73±7.23) in cows and (56.10±19.81) in sheep, with a statistically significant difference (P<0.05). There was a weak relationship between animal species and the development rate of hydatid cysts (p=0.05). The prevalence of hydatid cysts in sheep was higher than in cows, which may be due to a specific time division of the study. The highest percentage was obtained for fertile liver cysts (54.85%) and the lowest percentage for sterile cysts (14.85%). Moreover, calcified cysts had the highest rate following fertile cysts (30.28%). The significant fertility rate of liver cysts in sheep and lung cysts in cows, and protoscoleces viability of sheep indicates the importance of these two animals in terms of epidemiology and spread of hydatidosis in the region. The findings show that the prevalence of this disease is high in the region. It is worth mentioning that the authorities can largely eliminate the infected organs in the slaughterhouses by taking preventive measures, which will help reduce the disease development process.