In the course of hepatitis B, serum concentrations of the virus usually fall following sero-conversion, characterized by the loss of HBe antigen and appearance of detectable anti-HBe. However, hepatitis B viremia may persist even after sero-conversion. We assessed the association of continuous viremia with the precore (PC) (G1896A) mutation, basic core promoter (BCP) (A1762T, G1764A) mutations, the viral genotype and the quantity of viral DNA. Neither PC nor BCP mutations were detected in the viral DNA isolated from cases in which HBV became negative during the course of infection. The virus quantity increased after sero-conversion in all of the cases of persistent viremia with HBV genotype C harboring BCP mutations, indicating that the BCP mutation in genotype C is a determinant of continuous viremia. This feature was not evident in infections with HBV genotype B. Although the PC mutation was detected in the viral DNA from both genotypes B and C in continuous viremia, the mutation was not relevant to the quantity of virus. Our data suggest that HBV genotype C has a predisposition to acquire BCP mutations and these mutations activate virus replication after sero-conversion. This mechanism may be a cause of the poor prognosis of hepatitis with HBV genotype C. In conclusion, analyses of HBV genotype and BCP mutations are imperative to determine the prognosis of hepatitis B.