Sheep is one of the important hosts for hydatidosis in Iran as a hyperendemic region worldwide. In the present study, the efficacy of counter immuno-electerophoresis (CIE) and PCR tests to detect sheep hydatid cyst infection was carried out. For this, soluble antigen was provided using hydatid cyst fluids (HCFs). Blood sera were taken from a total number of 100 slaughtered sheep. CIE analysis was undertaken using negative and positive controls. DNA was extracted from protoscolices and a 1213bp fragment length of co1 gene amplified. Necropsy findings indicated that lung and liver of slaughtered sheep (33%) was infected with hydatid cyst. While it was 29% in CIE and 28% in PCR test. According to the necropsy findings as a gold standard test, sensitivity and specificity of CIE was 79.31% and 92.2%, respectively. Sensitivity and specifity of PCR test were determined 85.19% and 94.8%, as well. Data analysis showed that there is no significant difference between these two techniques (P<0.05). Based on these results, CIE technique can be considered as a useful method to screen sheep hydatid cyst infection.