There has been no report on the genotype-dependent regional, especially prefectural, differences in hepatitis C treatment in Japan. We conducted a retrospective cohort study using the nationwide database. The registration period of the database was from December 2009 to April 2013. Individuals with chronic hepatitis C were identified from the database. The sustained virologic response (SVR) rates in each prefecture were calculated stratified by genotype. Confounding variables were identified using stepwise logistic regression analysis. The range of the point estimate of the adjusted odds ratio explained prefectural differences in treatment outcomes. During the registration period, 36 prefectures registered cases to the database. A total of 16349 cases were registered and 11653 cases were included in the analysis. The mean age was 57.9±10.5 years; 7950 (68.2%) had hepatitis C virus (HCV) genotype 1 and 3703 (31.8%) had HCV genotype 2. The range in SVR rates was 30.0 to 63.0% for genotype 1 and 55.0 to 100.0% for genotype 2. In the multivariate analysis, the ranges of the adjusted odds ratio of each prefecture were 0.658 to 2.125 for genotype 1 and 0.364 to 2.630 for genotype 2. Our results suggest that regional, particularly prefectural, differences in chronic hepatitis C treatment with peg-interferon (IFN) and ribavirin (RBV) exist in Japan and that these regional differences may similarly exist both in HCV genotypes 1 and 2. Additional studies using these methods, considering medical situations in each prefecture and new treatments regimens, could greatly contribute to improving and standardizing chronic hepatitis C treatment.