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Cystic echinococcosis (hydatid disease) arising from infestation with a larval or adult form of the Echinococcus granulosus tapeworm is endemic in certain states of India, but affecting interventricular septum (IVS) solitarily is a scarce phenomenon. We present a rare case of transesophageal echocardiography guided management of IVS hydatid cyst even during cardiopulmonary bypass, which presented with a rather unusual complaint of repeated syncope.