Human herpes virus 6 (HHV6) has attracted attention in recent years as an important causative agent for limbic encephalitis after bone marrow transplantation (BMT). We report an autopsy case of HHV6-induced encephalomyelitis that developed after BMT. The patient was a 61-year-old man with acute myeloid leukemia, who developed disorientation and short-term memory disturbance 35 days after allogenic BMT. MRI demonstrated T1-weighted high-signal intensity lesions in the medial temporal lobe and thalamus, and PCR of the CSF disclosed an increase in the copy numbers of the HHV6 genome. The patient died after a clinical course of 6 months, and at autopsy the brain showed remarkable atrophy of the hippocampus. Histopathologically, neuronal loss with astrocytosis and patchy necrosis with infiltration of macrophages were found predominantly in the hippocampus, amygdala, mamillary body, claustrum, and thalamus. Perivascular and intraparenchymal lymphocytic infiltration was slight. Similar lesions were also scattered in the cerebral neocortex, midbrain, pontine base, cerebellar white matter, and lumbar cord. In some of these lesions, axons were relatively preserved in comparison with myelin sheaths. Significant increase in the copy numbers of the HHV6 genome was demonstrated in the postmortem brain tissue by PCR. Neuropathological features of the present case were similar to those described in previously reported cases, but the distribution of lesions was more widespread. Demyelination was supposed to be involved in the pathogenesis of some of the lesions.