The organic anion transport system in the choroid plexus is responsible for excretion of organic anions from brain to plasma. Disruption of this system could then result in accumulation of encephalopathic acyl groups in brain in a variety of metabolic disorders. Octanoate produced inhibition of this transport system associated with disruption of mitochondrial ultrastructure. Octanoylcarnitine and L-carnitine had no effect. These compounds represent those seen in the medium chain acyl CoA dehydrogenase deficiency. L-Carnitine may be useful for protecting the central nervous system through formation of the non-toxic acylcarnitine in this and other metabolic disorders characterized by accumulation of encephalopathic metabolites.