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To investigate the relationship between the genotypes of hepatitis B virus and the clinical and liver pathological features of patients with chronic hepatitis in the Zhoushan Islands.One hundred eighty HBV DNA positive chronic hepatitis patients with HBV markers were enrolled in this study. They were at least second generation Zhoushan Island residents. One hundred forty-seven of them were males and 33 were females with an average age of 39.0+/-11.3. Among the 180 patients, 17 had ASC, 57 had mild CHB, 48 moderate CHB, 9 severe CHB, 6 SHB, 39 LC, and 4 had HCC. The genotypes of their serum HBV were detected by using PCR integrated with Tagman MGB probe technology, and their serum HBV markers, HBV DNA and liver functions were also examined. Out of 180 patients, 129 accepted a liver biopsy. A pathological evaluation was then performed.HBVs of genotype C, 135 cases (75.0%), of B, 40 cases (22.2%), and of B+C, 5 cases (2.8%) were found among these 180 patients. No genotype A or D HBV were found. The proportions of genotype C virus were 7/17, 86/114, 34/39, 6/6 in ASC, CHB, LC and SHB patients. In the hepatocellular carcinoma patients, there were 2 each of genotype B and C. Among the 99 patients with genotype C HBV, 84 cases (84.8%) showed moderate and severe inflammation histologically in their livers and among the 30 patients with B, 7 cases (23.3%) showed moderate to severe inflammation in their livers (z = 6.47, P less than 0.01). The proportion of genotype C HBV was significantly different from that of genotype B HBV in those that showed moderate and severe (S3-4) liver fibrosis. In patients infected with genotype C HBV who had moderate and severe liver pathological changes, their clinical manifestations reflected better the histological alterations of their livers.Genotypes C, B and B+C HBV were found in CHB patients in the Zhoushan Islands of China, and type C was the predominant one. The liver pathological damage level of genotype C HBV infected patients is more serious than that of genotype B.