Detection and quantification for hepatitis B virus (HBV) DNA has been an essential tool in the clinical setting. We aimed to assess clinical performance of the RealArt HBV TM PCR (RealArt) assay and the COBAS TaqMan HBV (COBAS) assay. Serum levels of HBV DNA in 146 treatment-naïve chronic HBV (CHB) Taiwanese patients (118 males, 47 HBeAg + ; mean age, 34.7+/-13.0 y) were determined by both assays. The detection rate by the RealArt assay was 85.6% (125/146), which was not significantly different from the COBAS assay (89.7%, 131/146). The detection rate was also not significantly different between both assays irrespective of HBeAg seropositivity. The 2 assays were also comparable regarding quantification rate (92.8%, 116/125 vs 93.1%, 122/131). There was a positive correlation in the 109 specimens measurable by both assays (r=0.94,p<0.001). The mean HBV DNA level measured by the COBAS assay was significantly higher than the RealArt assay (5.24+/-1.83 vs 4.79+/-2.09 log IU/ml, p<0.001). This study demonstrated that both RealArt and COBAS assays were comparable regarding clinical performance in HBV DNA measurement.