Cystic Echinococcosis (CE) is a type of zoonotic infection that can be caused by a specific form of a parasite called Echinococcus granulosus sensu lato. Mainly, imaging techniques are utilized to diagnose CE. Serological tests are only used when imaging findings are atypical. Additionally, laboratory assays including, direct microscopy and PCR are used to confirm of diagnosis after treatment though obtained negative results with these tests cannot be ruled out the diagnosis. Specific miRNAs produced by the parasite could be used as markers to diagnose and monitor CE. This research investigates the diagnostic potential of parasite-derived miRNAs compared to the presence of protoscolex in animal-derived hydatid cyst samples. Accordingly, egr-let-7-5p, egr-miR71-5p, and egr-miR-9-5p were positive in 26, 25, and 11 out of 30 samples (86.6%, 83.3%, and (36.6%), respectively. There was no relationship between protoscolex presence and detection of either egr-let-7-5p or egr-miR-9-5p (p>0.05). On the other hand, egr-miR71-5p positivity was found to be statistically significant compared with protoscolex presence (p=0.04). As a result, egr-miR-71 is a promising potential target for the diagnosis of CE. Additional research is necessary to assess the diagnostic value of miRNAs in CE using a larger group of samples.