Twenty six infants and children with acute encephalitis and encephalopathy during two influenza seasons in Hokkaido, the northernmost island of Japan, were reported. Thirteen patients died and 5 had residual neurological sequelae. Influenza virus genome was detected by PCR in 9 out of 10 cerebrospinal fluid samples from these patients. CT and MRI of the brain demonstrated symmetrical changes in the thalamus and brainstem. The prevalence of these encephalitis and encephalopathy of childhood should be surveyed by nationwide scale.