Quantitation of low hepatitis B virus (HBV) DNA levels in patients with chronic hepatitis B is important for monitoring natural history of disease and treatment efficacy. This study aimed to compare the quantitation range and analytical sensitivity of the newly developed COBAS TaqMan™ HBV test (TaqMan test) with the COBAS Amplicor™ HBV Monitor Test (Amplicor test), using the Eurohep HBV reference plasma and serum samples from patients. Serial dilutions (2.7 × 101–2.7 × 108 copies/ml) of the Eurohep HBV reference plasma and 50 serum samples from chronic hepatitis B patients were tested by both assays. The TaqMan test could detect seven (2.7 × 102–2.7 × 108 copies/ml) of eight dilutions of the reference plasma, while the Amplicor test could only detect three of them (2.7 × 103–2.7 × 105 copies/ml). The HBV DNA values measured by the TaqMan test correlated very well with the theoretical Eurohep standard values (r = 0.998, P < 0.001). There were good correlations between the HBV DNA levels measured by the two assays on both the Eurohep reference plasma (r = 0.993, P < 0.001) and serum samples from patients (r = 0.904, P < 0.001). Compared to the Amplicor test, the TaqMan test had a higher sensitivity (50 vs. 300 copies/ml), shorter assay time (6 vs. 10 hr), and wider dynamic range (8 vs. 3 logs), and was more cost-effective in a clinical setting. These data indicate that the TaqMan test is an excellent tool for HBV DNA quantitation. J. Med. Virol. 77:486–490, 2005. © 2005 Wiley-Liss, inc.