OBJECTIVE To investigate hepatitis B virus (HBV) subtypes in patients chronically infected with genotype B or C of hepatitis B virus in Guizhou and to study the relationship between the subtypes and the progression of their liver diseases. METHODS Using PCR, 309 bp gene fragments in the HBV p region were amplified. The products of PCR were digested by VspI, NciI, BstEII and subjected to agarose gel electrophoresis. The subtypes of C1 and C2 were detected by restriction fragment length polymorphism (RFLP). B subtype was determined by direct sequencing of PCR product. One hundred seventy-eight patients with genotype B or C HBV infection in Guizhou, including 50 asymptomatic carriers (ASC), 100 chronic hepatitis (CHB), 14 liver cirrhosis (LC), and 14 hepatocellular carcinoma (HCC) patients were examined. The relationship between HBV C subtypes and the progression of their liver diseases was studied by analyzing the HBeAg positivity, HBV DNA loads and ALT levels of the patients. RESULTS Of 84 patients with HBV genotype C, 27 (32.14%) and 56 (66.67%) were subtype C1 and C2, respectively. In 94 genotype B, 93 (98.94%) were subtype Ba and only one was subtype Bj. Subtype C1 showed a trend of gradual decrease from ASC and CHB to LC/HCC groups. In contrast, subtype C2 showed a gradual increase (trend) in the same order. The HBeAg positivity was significantly lower in subtype C1 than that in subtype C2. The ALT levels and HBV DNA loads were higher in patients with subtype C2 than those in subtype C1, however no statistical significance was found in these primes (t=0.95, 0.79). CONCLUSIONS Subtype Ba is major and subtype C2 is more common in Guizhou. The distribution of subtype C1 and C2 are different in various stages of liver disease. The PCR-RFLP method is simple and accurate and can be used in a large-scale survey.