We have previously shown that hepatitis B virus (HBV) replication is controlled by noncytolytic mechanisms that depend primarily on the effector functions of the CD8 ؉ T cell response, especially the production of IFN-␥ in the liver. The mechanisms that control the nuclear pool of viral covalently closed circular DNA (cccDNA) transcriptional template of HBV, which must be eliminated to eradicate infection, have been difficult to resolve. To examine those mechanisms, we quantitated intrahepatic HBV cccDNA levels in acutely infected chimpanzees whose virological, immunological, and pathological features were previously described. Our results demonstrate that the elimination kinetics of the cccDNA are more rapid than the elimination of HBV antigen-positive hepatocytes during the early phase of viral clearance, and they coincide with the influx of small numbers of IFN-␥ producing CD8 ؉ T cells into the liver. In contrast, terminal clearance of the cccDNA is associated with the peak of liver disease and hepatocellular turnover and with a surge of IFN-␥ producing CD8 ؉ T cells in the liver. Collectively, these results suggest that cccDNA clearance is a two-step process mediated by the cellular immune response. The first step reduces the pool of cccDNA molecules noncytolytically, probably by eliminating their relaxed circular DNA precursors and perhaps by destabilizing them. The second step enhances this process by destroying infected hepatocytes and triggering their turnover. Surprisingly, despite this multipronged response, traces of cccDNA persist indefinitely in the liver, likely providing a continuous antigenic stimulus that confers lifelong immunity.H epadnaviruses are small enveloped hepatotropic DNA viruses containing a relaxed circular DNA genome, which is converted into a covalently closed circular DNA (cccDNA) episome in the nucleus of infected cells (1). The cccDNA molecule serves as the transcriptional template for production of viral RNAs that are exported to the cytoplasm and encode the viral structural and nonstructural proteins, including the reverse transcriptase͞DNA polymerase. Reverse transcription of the viral pregenomic (pg)RNA and second-strand DNA synthesis occurs in the cytoplasm within viral capsids formed by the HBV core protein (HBcAg). Capsids containing the mature relaxed circular DNA genome are either enveloped and exported as virions, or they deliver their DNA content to the nucleus, thereby amplifying the pool of cccDNA molecules to 10-50 copies per cell (2-5). The factors that regulate the cccDNA content of infected cells are not very well understood. In the duck hepatitis B virus (DHBV) model, the cccDNA level is regulated by the viral envelope proteins (6). Evidence from the woodchuck hepatitis virus (WHV) system suggests that cccDNA clearance is tightly associated with the destruction and turnover of infected hepatocytes (7,8). The possibility that cccDNA may also be susceptible to control by immune-mediated noncytolytic mechanisms is an open question at this time, at least partiall...