We report a neonate with isolated cytochrome c oxidase (COX) defect and severe multisystemic involvement. The patient had severe encephalopathy, predominant since birth, and died due to hypoxic-ischemic myocardiopathy. He was the second son of non-consanguineous, healthy parents who also had a daughter with chronic encephalopathy. The neonate presented dysmorphic phenotype, hepatic and muscular involvement, and possibly tubular involvement. Metabolic studies revealed markedly increased lactic/pyruvic concentrations. Diagnosis was based on muscular enzymatic studies and ultrastructural mitochondrial anomalies, while the mitochondrial DNA and results of the COX technique were normal. Histological examination revealed a massive subendocardial infarction. Aspects of this entity with relevance for genetic counseling are discussed.