OBJECTIVES: To evaluate patients with chronic hepatitis B virus (HBV) infection and low-level viraemia in terms of determining HBV DNA cut-off values and levels of alanine aminotransferase (ALT) and other possible markers for discriminating between chronic hepatitis B e-antigen (HBeAg)-negative patients and hepatitis B surface antigen (HBsAg) inactive carriers. METHODS: HBV-infected patients who were HBeAg-negative with undetectable HBV DNA by standard hybridization assay and high (HBeAg-negative group, n = 81) or normal (HBsAg inactive carrier group, n = 77) ALT levels were enrolled. Quantitative polymerase chain reaction assay using a COBAS Amplicor HBV monitor test was performed to detect low HBV DNA levels. RESULTS: The HBV DNA level was found to be significantly higher in the HBeAg-negative chronic HBV group (mean +/- SD 94 477 +/- 167 528 copies/nil) compared with the HBsAg inactive carrier group (mean +/- SD 19 215 +/- 57 970 copies/ml). CONCLUSIONS: A low level of viral replication may persist in chronic HBV-infected patients who are HBeAg-negative, and the level of HBV DNA was higher in the HBeAg-negative group than in the inactive HBsAg carrier group. Necroinflammation also persisted in the HBeAg-negative group and these patients had a higher level of ALT than the inactive HBsAg carriers.