Hypertrophic cardiomyopathy typically presents as an isolated cardiac lesion. Transient hypertrophic cardiomyopathy in infancy has been described as a result of exposure to maternal metabolic disorders or to corticosteroids. In addition, hypertrophic cardiomyopathy has been described in association with genetic syndromes and, in rare cases, as a primary lesion associated with other congenital heart defects. We describe the unusual association of hypertrophic cardiomyopathy and complete atrioventricular canal defect in an infant with trisomy 21.