To examine the relationship of hepatitis B virus (HBV) DNA sequences in the liver with histopathologic features and antigenic markers, the authors determined the hepatocytic status of viral DNA by in situ hybridization in formalin-fixed liver sections using a biotinylated probe in 45 patients with various chronic liver diseases. The results were compared retrospectively with the HBV serologic markers and histopathologic features including the presence of ground-glass cells or Shikata staining positivity. The specificity of this in situ detection of HBV DNA has been proven excellent in a double-blind control study in 18 patients in whom liver HBV DNA was also determined by DNA extraction, gel electrophoresis, and the Southern blotting technique. In 41 patients, the findings of HBV DNA and serologic markers were concordant (17 positive and 24 negative). Twelve of the 20 HBV-DNA-positive patients were HBsAg-positive (6 with chronic hepatitis, 3 with cirrhosis, and 3 with hepatocellular carcinoma). Ground-glass cells or Shikata positivity were found in 10 of these 12 patients. HBV DNA sequences were found in the liver of all patients with chronic liver disease and serologic positivity for HBV infection. In liver with normal histologic features, HBV DNA was not demonstrable, despite the positive anti-HBc and anti-HBs. However, a positive HBV DNA was found in 3 serologically negative patients. In another patient the interpretation of findings was impossible because of severe hemosiderosis. From this study, it is concluded that in situ detection of HBV DNA in formalin-fixed liver sections has a clinical value and is suitable for routine use.