This study was conducted to estimate the fertility of hydatid cysts and viability of protoscoleces based on the location, size and type of cysts in slaughtered animals in Qazvin, Iran. Cysts were collected from the livers and lungs of 247 sheep and 275 cattle infected with hydatid cysts. Fertility of the cysts was assessed by examining the cysts' fluid for the presence of protoscoleces and the viability of the protoscoleces was determined using staining with an aqueous solution of 0.1% eosin. The highest and lowest rate of fertility was observed in hepatic cysts of sheep (81.05%), and cattle (1.27%) respectively. Most fertile cysts had medium size (45.03%), while the lowest fertility rate belonged to the small cysts (22.8%) . Relationship between fertility of the cysts and type of infected organs, type of animals and size of cysts were significant (p<0.05). The highest rate of viability was found in cattle's lungs (88.06%) and the lowest rate was seen in sheep's liver cysts (46.49%). There was significant difference in viability of fertile cysts between cattle and sheep organs (p<0.05). Most of sterile, suppurative and calcified cysts were found in cattle's lungs (84.7%), cattle's liver (89.87%) and sheep's liver (6.58%) respectively.In conclusion it can be said that fertility rates of liver and lung hydatid cysts of sheep and viability of their protoscoleces is considerable. In addition, although the fertility of cysts in cattle was low, but they had high viability rate.