Human herpesvirus-6 (HHV-6) infection is common in infancy, and symptoms are usually mild. However, encephalitis and other neurologic complications have been reported. Primary HHV-6 infection has been rarely confirmed in the central nervous system. We studied 21 children with suspected HHV-6 infection, drawn from a prospective, large-scale study of neurologic infections in Finland. Human herpesvirus-6 polymerase chain reaction was performed on cerebrospinal fluid samples, and antibody tests were performed on serum and cerebrospinal fluid. We identified nine children, aged 3 to 24 months, who had HHV-6-specific nucleic acid in cerebrospinal fluid. Primary infection was confirmed by seroconversion of specific antibodies in six, whereas one had a fourfold increase, and one had a fourfold decrease, in the antibody titer supporting recent infection. Generalized and prolonged seizures appeared in six children, four had a rash, four had ataxia, and four had gastroenteritis. All but two had a high fever. At follow-up, four children had evident neurologic sequelae, ataxia, and developmental disability, and needed special education. Primary HHV-6 infection may invade the central nervous system, and can cause neurologic symptoms and potentially permanent disability in children aged <or=2 years. The possibility of HHV-6 infection must be considered when treating acutely ill children, and especially those with convulsions.