An in vitro and in vivo study was conducted to show the effect of dipeptide methyl ester on the protoscolices of Echinococcus granulosus and in naturally infected sheep. Easily punctured cysts were located by ultrasonography. A PAIR and PAI method were performed by the injection of dipeptide methyl ester into these cysts at a final concentration of 110 mmol/L. Follow-up was conducted monthly by ultrasonography. After injection of the compound, the sheep were sacrificed at different times from 6 to 17 weeks. The size and the morphological aspect of treated cysts were noted. Samples were collected for histology and electron microscopy. In conclusion, these studies revealed significant and rapid detachment of the membrane of the treated cyst and alteration of the inner membrane in less than 5 min after injection of the drug, confirming the effect of the compound on the laminated layer of the parasite.