Cystic Echinococcosis (CE) caused by the larval stages of taeniid cestodes of the genus Echinococcus is a neglected helminth zoonosis affecting humans and various animal species. The aim of this study was to assess the fertility of cattle from two provinces in the northeast and southwest of Iran, and molecularly characterize the hydatid cysts collected from them. From 5000 carcasses of naturally infected cattle inspected from October 2013 to December 2015, 70 hydatid cysts were collected in Mashhad in the northeast and 50 from Ahvaz in the southwest. All 120 samples were identified as E. granulosus senso stricto (G1, common sheep strain) by PCR-RFLP analysis and sequencing of the ITS1 gene. All cysts recovered from these animals were sterile, highlighting the lower importance of cattle in the transmission of the “sheep strain”. The fact that that the zoonotic E. granulosus s.s. is dominant makes CE an important public health concern in Iran.