We report hypertrophic cardiomyopathy in a newborn with congenital cytomegalovirus infection. The neonate had distinct signs of congenital cytomegalovirus infection including petechiae, jaundice, intracranial calcifications, cerebral ventriculomegaly and chorioretinitis together with hypertrophic cardiomyopathy. Following determination of anti-cytomegalovirus IgM, viral DNA was also isolated from the plasma of the patient by polymerase chain reaction. Although cytomegalovirus is a relatively frequent cause of myocarditis in childhood, it was rarely reported to be associated with cardiac abnormalities such as structural heart disease, atrioventricular block, or dilated cardiomyopathy. To our knowledge, this is the first case with congenital cytomegalovirus infection and hypertrophic cardiomyopathy.