Human herpesvirus 6 (HHV-6) has recently been recognized as an important pathogen in immunocompromised hosts, such as patients who have undergone allogeneic bone marrow transplantation (allo-BMT). Here we report a case of HHV-6 meningoencephalitis in a patient who underwent allo-BMT from an HLA-identical sibling. The patient suffered from headache, high fever, tremor, and disorientation on day 35 after allo-BMT. Findings at magnetic resonance imaging, electroencephalography, and routine cerebrospinal fluid (CSF) examination suggested the presence of viral meningoencephalitis. We diagnosed HHV-6 meningoencephalitis by means of polymerase chain reaction (PCR) analysis of a CSF specimen. Successful treatment was achieved with ganciclovir. Because HHV-6 encephalitis has a potentially fatal and fulminant course, it is necessary that HHV-6 encephalitis be recognized as one of the central nervous system complications that can follow allo-BMT. PCR analysis for HHV-6 in the CSF specimen is necessary for appropriate diagnosis and treatment.