The “stone heart” syndrome is a rare but often fatal complication of cardiac surgery associated with hypertrophy of the myocardium. The mechanisms behind the syndrome are not fully understood. In this case report, we describe two cases of stone heart in newborn girls. Both girls were born with congenital heart abnormalities including ventricular septum defects (VSD), hypertrophy of the myocardium and patent arterial duct (PDA), which was prenatally diagnosed. In each of the two cases, the stone heart became evident immediately after initiating cardiopulmonary bypass, and ended fatally.