We report a patient who showed pathological features of both multiple system atrophy (MSA) and progressive supranuclear palsy (PSP) at autopsy. The clinical features included severe cerebellar ataxia, autonomic failure, and rigid-akinetic parkinsonism. The clinical diagnosis was MSA. Pathological examination showed severe neuronal loss with gliosis in the putamen, substantia nigra, inferior olive, and the pontine nucleus, and numerous glial cytoplasmic inclusions. In addition, moderate neuronal loss with gliosis was observed in the globus pallidus and subthalamic nucleus, and neurofibrillary tangles and tufted astrocytes were seen in the basal ganglia and the brain stem. These findings indicate that the patient had both MSA and PSP. Double-labeling immunofluorescence in the brain stem showed alpha-synuclein immunoreactivity localized in the oligodendrocytes and phosphorylated tau immunoreactivity in the neurons and the glia. Co-existence of synucleinopathy and tauopathy is rare.