It is well known that hepatitis B virus infections can be transient or chronic, but the basis for this dichotomy is not known. To gain insight into the mechanism responsible for the clearance of hepadnavirus infections, we have performed a molecular and histologic analysis of liver tissues obtained from transiently infected woodchucks during the critical phase of the recovery period. We found as expected that clearance from transient infections occurred subsequent to the appearance of CD4 ؉ and CD8 ؉ T cells and the production of interferon gamma and tumor necrosis factor alpha in the infected liver. These events were accompanied by a significant increase in apoptosis and regeneration of hepatocytes. Surprisingly, however, accumulation of virus-free hepatocytes was delayed for several weeks following this initial influx of lymphocytes. In addition, we observed that chronically infected animals can exhibit levels of T-cell accumulation, cytokine expression, and apoptosis that are comparable with those observed during the initial phase of transient infections. Our results are most consistent with a model for recovery predicting replacement of infected hepatocytes with regenerated cells, which by unknown mechanisms remain protected from reinfection in animals that can be cured.Human hepatitis B virus (HBV), as well as the related woodchuck hepatitis virus (WHV), can cause transient or chronic infections in its native host (11,24,27). The molecular basis for the dichotomy of disease outcomes is not known. As in humans, in woodchucks chronic, lifelong WHV infections generally occur when virus is transmitted during or soon after birth. Infection of adults leads to transient infections in over 90% of cases. Experiments with woodchucks have shown that clearance of infections can occur within a few weeks even when nearly all hepatocytes in the liver have been infected (14, 20). Thus, a major question concerns the molecular mechanism responsible for the regulation of clearance of virus from infected hepatocytes.Clearance from infections with noncytopathic viruses, such as hepadnaviruses, requires the elimination of infected cells by cytotoxic T lymphocytes (CTLs) and the production of neutralizing antibodies directed against one or several viral proteins (13). A role for T cells in the recovery from natural hepadnavirus infections has been demonstrated through treatment with cyclosporin A, a known suppressor of T-cell function, which prevents recovery from otherwise transient WHV infections in adult woodchucks (4). It also appears that the number of CTLs present in the peripheral blood of chronically infected patients is approximately 10 to 100 times lower than that in the blood of patients with transient infections (23), suggesting that a critical number of reactive CTLs are required for recovery. In this scenario all infected hepatocytes would have to be killed by CTLs and replaced by uninfected cells. In order to sustain sufficient liver function, the rate of cell death should not exceed the rate of cell replacement ov...