Influenza-associated encephalopathy is often reported in young Japanese children, but its pathogenesis is unknown. Although influenza virus can be demonstrated by throat culture for patients with encephalopathy, cultures of samples of cerebrospinal fluids (CSF) do not yield the virus. Eight patients with encephalopathy or complicated febrile convulsions had influenza virus infection diagnosed by means of culture, polymerase chain reaction (PCR), or rapid diagnosis using throat swabs. In all 8 cases, the results of PCR testing of CSF specimens for influenza virus were negative. On the other hand, human herpesvirus 6 (HHV-6) DNA was demonstrated in CSF specimens obtained from 2 of 8 patients. In 3 of 8 patients, the presence of human herpesvirus 7 (HHV-7) DNA was demonstrated in CSF specimens. Some cases of influenza-associated encephalopathy reported in Japan may be attributable to a dual infection with influenza virus and HHV-6, -7, or both. Another possibility is that latent HHV-6 or HHV-7 in the brain is reactivated by influenza, causing encephalopathy or febrile convulsions.