The correlation of hepatitis C virus genotypes and the development of hepatocellular carcinoma is still controversial. The most pertinent studies are conducted by seroepidemiological methods. It has been suggested that tissue RT-PCR may be more efficient than serological testing for hepatitis C virus RNA. The purpose of this study was to investigate the infectious status of hepatitis C virus genotypes in hepatocellular carcinoma tissue for revealing the role of hepatitis C virus genotypes in carcinogenesis of hepatocellular carcinoma. Hepatitis C virus genotypes in cancerous and noncancerous liver tissues of 95 Chinese patients with hepatocellular carcinoma were analyzed by a modified type-specific in situ reverse transcription polymerase chain reaction (RT-PCR) method. Hepatitis C virus genotypes were simultaneously examined by Okamoto's method using extracts from hepatocellular carcinoma tissues. The hepatitis C virus genotypes in hepatocellular carcinoma tissues were found including 1b, 2a, mixed type (1b+2a) and 3a in 13, 23, 2 and 4 samples respectively. There was no significant difference in either the positivities between 1b (13.7%, 13/95) and 2a (24.2%, 23/95) (P>0.05) or the staining intensity and distribution of positive cells between 1b and 2a (p>0.05). No statistically significant difference was found between the two virus genotypes in main clinico-pathologic parameters of hepatocellular carcinoma. The localizations of hepatitis C virus RNA-positive signals were mainly cytoplasmic (22/36) in noncancerous regions, but nucleocytoplasmic (19/36) or nuclear (3/36) in cancerous regions. The positive nucleocytoplasmic/nuclear signals of genotype 1b (11/13) in hepatocellular carcinoma were seen more frequently than those of genotype 2a (11/23) (P<0.05). The discordant hepatitis C virus 2a and 1b positivities in serum samples and in cancerous tissues of hepatocellular carcinoma patients were also found, suggesting that the detection of serum hepatitis C virus genotypes in the patients with hepatocellular carcinoma may not reflect the actual status of hepatitis C virus genotypes in cancerous tissue. The pathogenetic significance of existence of hepatitis C virus gene in the nucleus of hepatocytes and malignant cells needs further investigation.