Primary human herpesvirus 6 infection is acquired mainly during the first two years of life and is often associated with febrile seizures. The aim of the present study was to investigate in Greece the frequency and clinical characteristics of primary human herpesvirus 6 (HHV-6) infection in hospitalized children with febrile seizures. Children aged from 6 months to 5 years without known neurologic disease were examined for primary HHV-6 infection, by real-time polymerase chain reaction in acute-phase plasma and by indirect immunofluorescent assay for antibody titers in acute and convalescent serum. Of 65 children included in the analysis, 55 experienced the first febrile episode of seizures and 10 the second. Primary HHV-6 infection was verified in 10 of 55 children with a first febrile episode (18%), whereas none of the 10 children with a second episode of seizures had primary HHV-6 infection. Eight children were infected with HHV-6 type B and two with type A. None of the 85 control subjects had primary HHV-6 infection, but 49% had immunoglobulin G antibodies against the virus. These findings suggest that primary HHV-6 infection is frequently associated with febrile seizures in children in this geographic region and should be considered, especially for a first episode of febrile seizures.