Human herpesvirus 6 (HHV-6) is a cause of roseola infantum. Recent reports associate HHV-6 with cases of encephalitis; however, conclusive etiologic data do not exist. We evaluated clinical data and laboratory specimens obtained from patients with focal encephalitis of unknown etiology. Cerebrospinal fluid (CSF) specimens were tested by polymerase chain reaction for the presence of HHV-6 DNA. Selected samples were analyzed by DNA sequencing. We detected HHV-6 DNA in the CSF of nine of 138 patients. DNA sequencing revealed that group B strains of HHV-6 were present in those specimens that were analyzed. No significant differences could be demonstrated in clinical presentation, laboratory findings, or neurodiagnostic imaging results between the nine patients with confirmed HHV-6 infection and the 129 patients without evidence of HHV-6 infection. Neurological outcome for the nine HHV-6-infected patients varied from complete recovery without neurological deficit to death. Further prospective study is warranted.