The geographic distribution of hepatitis B virus (HBV) genotypes in Japan and its clinical relevance are poorly understood. We studied 731 Japanese patients with chronic HBV infection. HBV genotype was determined by the restriction fragment length polymorphism (RFLP) method after polymerase chain reaction (PCR). Of the 720 patients with positive PCR, 12 (1.7%) were HBV genotype A, 88 (12.2%) were genotype B, 610 (84.7%) were genotype C, 3 (0.4%) were genotype D, and 7 (1.0%) were of mixed genotype. Over 94% of patients on the Japanese mainland had genotype C, while 60% of the patients on Okinawa, the most southern islands, and 22.9% in the Tohoku area, the northern part of the mainland, harbored genotype B. Compared with genotype C patients, genotype B patients were older (53.6 to 42.2 years; P <.01), had a lower rate of positive hepatitis B e antigen (HBeAg) (18.4% to 50.6%; P <.01), and a lower level of serum HBV DNA (5.02 to 5.87 log genome equivalents (LGE)/mL; P <.01). The mean age of the genotype B patients with hepatocellular carcinoma was 70.1 +/- 9.2 years, compared with 55.2 +/- 9.7 of genotype C patients (P <.01). These results indicate that genotypes C and B are predominant in Japan, and there are significant differences in geographic distribution and clinical characteristics among the patients with the different genotypes.