We studied promoter region polymorphisms in the tumor necrosis factor (TNF), interleukin (IL)-6, IL-10, and transforming growth factor (TGF)-beta1 genes in Japanese patients with multiple system atrophy (MSA) (n=122) and normal controls (n=277). The frequency of the TNF-1031C, a high producer allele of TNF, was increased significantly in MSA patients compared with controls (chi2=12.36, P=0.0021, Pc=0.0084). In contrast, there was no difference in the genotype or allele frequency in the other cytokine gene polymorphisms. We also failed to detect any difference in the disease onset between each genotype of the polymorphisms examined. Our findings suggest that TNF might have a toxic effect in MSA.