We carried out a molecular-based epidemiological survey of hepatitis viruses, including hepatitis B virus (HBV), hepatitis C virus (HCV), and hepatitis E virus (HEV), in Harbin, China. The study population of 358 subjects consisted of 132 healthy blood donors and 226 liver disease patients residing in Harbin City and surrounding suburbs. The infection rate of each virus among healthy subjects was 14.4% (19/132) for HBV and 2.3% (3/132) for HCV. In contrast, among liver disease patients, the infection rates were 72.6% (164/226) for HBV and 7.5% (17/226) for HCV, respectively (P < 0.01 and P < 0.05, respectively). In particular, nearly 64% of hepatocellular carcinoma patients in Harbin was found to be infected with HBV. The most common viral genotypes were HBV type C (80%) and HCV type 1b (31.3%). Interestingly, a high prevalence of the HBV pre-S1/S2 deletion mutant was found in 13 of 58 (22.4%) subjects. Moreover, testing for HEV among 202 subjects resulted in the detection of anti-HEV IgG in 53 cases (26.2%). The prevalence of anti-HEV IgG has already reached 20% in tested cases aged less than 10 years. These results suggest that HBV infection is widespread in Harbin, China and has led to a high incidence of acute and chronic liver disease in this region.