The clearance of the hepatitis B surface antigen (HBsAg) from serum usually indicates a resolution of biochemical and histological hepatitis in patients with chronic hepatitis B. 1 However, there are clearly documented cases of reactivation of latent viral infection following chemotherapy and immunosuppressive treatment, as well as de novo infection in patients receiving organs from HBsAg-negative donors with serological evidence of previous hepatitis B virus (HBV) infection. [2][3][4][5][6][7] In this setting, the reactivated infection is not entirely unexpected, because most patients who have cleared HBsAg from the serum still have detectable HBV DNA in the liver using the polymerase chain reaction (PCR) methodology. [8][9][10][11][12][13][14] In fact, HBV DNA can also be found in bodily secretions and peripheral blood mononuclear cells from patients with acute and chronic HBV infection after sustained loss of serum HBsAg. [15][16][17] Taken together, these studies suggest that following the loss of HBsAg from serum, HBV persists in a state of low-level replication or in a replication-competent state that can be reactivated to form infectious particles.The natural biology of the latent virus may be further investigated by assessing the transcriptional activity and the molecular form of the persistent HBV DNA. Using in situ hybridization, we were unable to detect hepatic HBV RNA in patients who had cleared serum HBsAg, and other investigators had little success using reverse-transcription (RT) PCR studies because of the inability to completely eradicate tissue HBV DNA. 11 Furthermore, the molecular form of the persistent HBV DNA has proved difficult to define because of the minute quantities of virus found in patients with resolved hepatitis.During chronic infection, HBV DNA can be detected in four predominant molecular forms. Following infection by the intact Dane particle, the partially double-stranded HBV-DNA genome becomes a covalently closed circular (CCC) DNA molecule that acts as a template for transcription of mRNA and the RNA pregenome. The reverse transcription of the RNA pregenome and second-strand HBV DNA synthesis results in low-molecular-weight replicative intermediates, whereas the HBV DNA that integrates into the host' s genome can be detected as high-molecular-weight species on Southern blot. 18,19 Similar to retroviral integration at the site of the long terminal repeats, HBV DNA generally inserts into DNA flanked by the direct repeat regions, which share sequence homology with the U5 region of murine leukemia virus long terminal repeats. [20][21][22] The genomic organization of the HBV direct repeat region provides a potential strategy for the detection of replicating virus when only minute quantities of HBV DNA are present (Fig. 1). Using PCR primers flanking the direct repeat region, the CCC HBV DNA can be amplified using PCR. In contrast, the HBV DNA within the Dane particle is incomplete, and integrated HBV DNA is usually, but not always, disrupted in the direct repeat region (Fig. 1). Th...