The persistence of covalently closed circular (ccc) DNA of Hepatitis B virus (HBV) in liver cells is believed to be the major reason for relapse after completion of HBV antiviral therapy. Up to now, there is no sensitive method to quantify cccDNA in infected liver cells. We designed a set of primers to specifically amplify DNA fragments from HBV cccDNA but not from viral genomic DNA. A good linear range was obtained when 100-10(7) copies of HBV cccDNA were used as template in the quantitative real-time PCR. Not only is this method rapid, economical, highly sensitive, it can be used to monitor HBV cccDNA in infected human liver biopsies and to guide patients undergoing long-term anti-HBV therapy.