To investigate neuronal damage in the cerebral cortex in patients with multiple system atrophy (MSA), immunohistochemical stainings were carried out on the prefrontal cortex, the hippocampus, the precentral gyrus, the supplementary motor cortex and the occipital cortex in 6 cases of MSA and 6 controls, using antibodies against ubiquitin, tau protein and neurofilaments (BF10, RT97, 147). In MSA cases, a variable number of neuronal ubiquitinated inclusions were observed in the granule cell layer of the dentate gyrus (316) and the prefrontal cortex (3/6). An increased number of ubiquitinated dots-like structures were also observed in the parahippocampal gyrus of MSA cases (4/6) in comparison with controls. These results showed further evidence of neuronal damage in the cerebral cortex in MSA and strongly suggest a relationship between the cerebral cortical pathology and occasional manifestation of cognitive deficits in some MSA cases.