To clarify the role of hepatitis B virus infection in HBsAg-seronegative patients with chronic liver disease and hepatocellular carcinoma in Taiwan, we examined the hepatitis B virus DNA in liver biopsy tissues of 112 patients by Southern blot analysis. The patients studied included 43 patients with nonalcoholic chronic liver disease, 21 patients with hepatocellular carcinoma and 48 control patients with other hepatobiliary and gastrointestinal diseases. To confirm the specificity of the intrahepatic hepatitis B virus DNA signal and to understand the structure of the integrated viral sequences, molecular cloning and DNA sequencing of an integrated hepatitis B virus DNA were done in one patient. Among 13 patients without serological evidence of previous hepatitis B virus infection, no hepatitis B virus sequences were found in the liver. In other HBsAg-negative patients with evidence of previous hepatitis B virus exposure, a substantial positive rate of intrahepatic hepatitis B virus DNA was found (7%). The intrahepatic hepatitis B virus DNA was all in integrated form. The positive rate among patients with nonalcoholic chronic hepatitis and cirrhosis (2%) was not different from that of the control group with other hepatobiliary and gastrointestinal diseases (4%). However, the positive rate of integrated hepatitis B virus DNA between hepatocellular carcinoma patients and nonhepatocellular carcinoma patients was statistically significant (19% vs. 3%, p less than 0.05). Molecular cloning and sequencing of a 3.0 kb EcoRI fragment of an integrated hepatitis B virus DNA from an anti-HBs-positive patient revealed that it was a partial copy of the hepatitis B virus genome.(ABSTRACT TRUNCATED AT 250 WORDS)