A 15-year-old boy presenting with epilepsy, optic atrophy and intracranial calcifications was diagnosed as having metaphyseal dysplasia by bone X-ray examinations. The patient had no laboratory data suggesting other metabolic or endocrinologic disorders. In addition, CT scans showed unique intracranial calcifications of the corpus callosum and periventricular and subcortical white matter, which were distinct from those of previously reported disorders. This case may represent a unique subset or a new type of metaphyseal dysplasia associated with intracranial calcifications and central nervous system symptoms.