Selection of HBsAg-positive patients for antiviral therapy requires an estimation of disease activity and viral replication. Serum transaminases and histological analysis are commonly used to assess disease activity, and viral replication is assessed by serological testing of HBeAg and serum hepatitis B virus (HBV) DNA. Dot blot hybridisation may be insufficiently sensitive to corroborate low-grade replication in patients with active hepatitis, and polymerase chain reaction (PCR) may be testing too sensitive for this role. Theoretically an assay of intermediate sensitivity is therefore required. Our aim was to evaluate whether the branched chain DNA (bDNA) assay would fulfil this function. Seventy-one HBsAg-positive patients were tested for HBV DNA by the bDNA assay; 64 were also tested by dot blot hybridisation and, when appropriate, also by PCR. Thirty-seven (52%) patients were positive for HBV DNA by the bDNA assay. HBV DNA was detected in the majority (21/28; 75%) of HBeAg-positive patients but also in 14 of 36 (39%) anti-HBe-positive patients. HBV DNA was detected by the bDNA assay in 20 of 48 (42%) patients negative for HBV DNA by dot blot hybridisation assay. All patients positive for HBV DNA by dot blot hybridisation were also positive by the bDNA assay. Sixteen of twenty-five (64%) patients negative for HBV DNA by the bDNA assay were positive for HBV DNA by PCR. The bDNA assay is a sensitive and reliable method for the detection of HBV DNA. As nucleoside analogue therapy becomes more widely available, the assay should provide a useful tool for the selection for and monitoring of patients on antiviral therapy.