Acute exacerbation (AE) of chronic hepatitis B is usually preceded by reemergence or increase of hepatitis B virus (HBV) in the serum. To investigate the origin of the reemergence or increase, we compared the identity of the serum viral genome to that in the liver and in previous AE by full-length sequencing. The full-length viral genome and extent of quasispecies were obtained from serum and liver biopsy specimens at the same time from 9 subjects with hepatitis B exacerbation (group I). Composition of viral quasispecies was compared by the genetic diversity and the average number of nucleotide substitutions within and between different viral sources. Another 2 patients with repeated AEs (group II) were also enrolled, and their serial serum alanine aminotransferase, HBV DNA levels and full-length sequences were determined. In all group I patients, serum viral genome was identical to that in the liver. The genetic diversity and the average number of nucleotide difference were also comparable between serum and liver tissue. In 2 group II patients, the viral variant that emerged after previous AE was not identical to that caused by the subsequent AE. Dominant viral strains for serial AEs in a single patient did not show a sequential evolution, but presented as a horizontal selection of a minor population from the original viral pool. In conclusion, the findings suggest that viral strain in serum reflects the intrahepatic strain of the AE. Random reactivation of the original HBV pool, rather than a sequential evolution of one strain, also contributes to the onset of repeated AE. A cute exacerbation (AE) occurs frequently in hepatitis B surface antigen carriers. 1 The exacerbation can accelerate the progression of liver disease. 2 Hepatitis B virus (HBV) evolves rapidly in chronic hepatitis B patients, and the correlation of HBV variation with the onset of AE has been extensively studied. [3][4][5] Previously, we investigated sequential full-length viral sequences in patients with AE 6,7 and found that most exacerbations were preceded by an upsurge of serum HBV identical to the preexisting HBV strain. After exacerbation, however, about half of the patients were repopulated by a different viral variant in the circulation.The pathogenesis of AE actually takes place in the liver. Therefore, it is better to directly characterize the viral genome from the liver biopsy specimen. As noted previously, some potential pathogenic strains may replicate actively within the liver but not be released into the circulation. 8 Thus, HBV genomic changes that are correlated with the development of hepatitis B exacerbation might occur and be retained within the liver but not be detected in the specimens obtained from the circulation. To resolve these questions, the representation of the serum viral genome to the corresponding intrahepatic one was first determined by comparing the dominant viral nucleotide sequence and genetic complexity of the viral quasispecies between both tissue specimens obtained si-