A 3-year 8-month-old girl died after 14 months of illness characterized by episodes of intermittent ataxia associated with oculomotor palsy, hypotonia, mental confusion, and disturbances of consciousness. In the last 4 months of life, there were signs of liver dysfunction. Pyruvate dehydrogenase and alpha-ketoglutarate dehydrogenase activities were normal in autopsy brain specimens and in cultured fibroblasts from the patient. Carnitine acetyltransferase was deficient in liver, brain, kidney, and cultured fibroblasts. Medium- and long-chain carnitine acyltransferase activities were normal. It is proposed that a functional defect of acetyl-coenzyme A (acetyl-CoA) utilization in brain mitochondria accompanies the carnitine acetyltransferase deficiency.