Hypertrophic cardiomyopathy (HCM) is a heterogeneous disorder characterized by thickening of the heart and an increased incidence of sudden death. This study is aimed to determine the genetic cause of severe cardiac hypertrophy in an infant. An infant was assigned a diagnosis of ventricular preexcitation and severe biventricular HCM requiring septal myectomy. Genetic testing showed a novel heterozygous E506Q mutation of the adenosine monophosphate (AMP)-activated protein kinase (PRKAG2) gene. Endomyocardial biopsy samples did not demonstrate significant glycogen accumulation. Hypertrophic cardiomyopathy due to PRKAG2 mutations may have a degree of cardiac hypertrophy exceeding that expected from observed amounts of glycogen deposition.