In systemic carnitine deficiency, an early phase of nonketotic hypoglycemia and liver dysfunction may precede a late phase of encephalopathy and myopathy. We studied two children with recurrent episodes of nonketotic hypoglycemia who were found to have systemic carnitine deficiency without myopathy or encephalopathy. Early institution of appropriate therapy prevented the onset of late debilitating complications in one patient, whereas therapeutic noncompliance in the other patient led to an episode of encephalopathy and myopathy. Metabolic studies indicated that decreased availability of alanine may be a factor in the genesis of hypoglycemia; concurrent depletion of cerebral glucose, ketones, and glycogen may be the cause of the encephalopathy.