Infantile cardiomyopathy is a genetically heterogeneous disorder with significant morbidity and mortality. We report four unrelated patients presenting as infants with isolated hypertrophic cardiomyopathy in whom a novel mitochondrial m.8528T>C mutation was identified. This results in a change of the initiation codon in ATPase6 to threonine and a concurrent change from a highly conserved hydrophobic amino acid, tryptophan, at position 55 of ATPase8 to a highly basic arginine. This is the first report of a mutation affecting both mitochondrial genome encoded Complex V subunit proteins. Testing of family members of one patient indicates that the mutation is heteroplasmic and correlated with disease. Mitochondrial genome sequencing should be considered in patients with infantile hypertrophic cardiomyopathy.