As suggested by concordance rates in twins, genetic factors are critical to the susceptibility and progression of primary biliary cirrhosis (PBC). Among cytokines, transforming growth factor beta-1 (TGF-β1) plays an important role in autoimmunity and liver fibrosis and a TGF-β1 receptor knockout mouse has been recently proposed as a model for PBC. The promoter region of the TGF-β1 gene has two single nucleotide polymorphisms (SNPs) at positions -800 and -509, which influence serum concentrations of latent and active TGF-β1. We studied genomic DNA from 65 Japanese patients with PBC and 71 matched healthy controls for the association of TGF-β1 SNPs analyzed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) with susceptibility and disease progression of PBC. The -800 G to A SNP was not found in the Japanese population and no significant difference in the distribution of TGF-β1 promoter gene -509 SNP was found between PBC cases and controls. Further, TGF-β1 genotypes failed to correlate with clinical parameters, including histological stage and prognostic score. In conclusion, the TGF-β1 promoter gene SNPs are not associated with disease susceptibility or progression in Japanese patients with PBC.