The role of hepatitis B virus (HBV) in carcinogenesis of hepatitis B surface antigen (HBsAg)-negative, anti-hepatitis C virus (anti-HCV)-positive hepatocellular carcinoma (HCC) remains unknown. To investigate the state of HBV DNA in such HCC, HBV DNA was examined by polymerase chain reaction (PCR) between HBV DNA and human Alu sequence (HBV-Alu PCR), which could detect integrated form of HBV DNA only, and by conventional HBV PCR, which could detect both integrated and episomal forms of HBV DNA. In all the 17 HBsAg-positive HCC, HBV DNA was detected by both HBV-Alu PCR method and conventional HBV PCR method. By contrast, in HBsAg-negative, anti-HCV-positive cases, HBV DNA was detected in 10 of 21 (47.6%) by conventional HBV PCR and in none of 21 (0%) by HBV-Alu PCR method. Thus, integrated form of HBV DNA was not found in most HbsAg-negative, anti-HCV-positive HCC in the current study. The role of episomal form of HBV DNA requires further investigation of its involvement in the process of the development of HBsAg-negative, anti-HCV-positive HCC.