To study the disease process in the brain in subacute sclerosing panencephalitis (SSPE), sequential changes in ferritin, creatine kinase (CK), and neopterin in the cerebrospinal fluid (CSF) of two patients with SSPE were compared with the changes in the clinical signs and symptoms and the findings by magnetic resonance imaging (MRI). On the basis of changes in various substances in the CSF, especially ferritin, CK and neopterin, we concluded that the high-intensity area in MRI might be evidence of local inflammation and the resulting cell damage. Ferritin, CK and neopterin seemed to be biochemical markers in patients with SSPE for detection of the extent of lesions, and their measurement may provide information useful for evaluation of the therapeutic response.