Cytochrome c oxidase (CCO) deficiency is associated with various types of mitochondrial encephalomyopathy. The enzyme activities in different tissues and organs are varied. We report an 11-year-old girl with CCO deficiency, who presented with nystagmus, ptosis and optic atrophy. Her younger sister died of respiratory failure at 7 years of age and had the same initial clinical manifestations. Their parents were consanguineous. The girl had mild mental retardation and frequent premature ventricular contractions. Brain magnetic resonance imaging of the patient on admission revealed multiple lesions in both the gray and white matter. Except for arrhythmia and marked right axis deviation of the heart on electrocardiography, no other evidence of cardiac involvement was noted. Although a muscle biopsy was normal for both histochemical stains and electron microscopy, the enzyme assays in cultured skin fibroblasts revealed partial CCO deficiency, which may explain the clinical presentations.