Background. Breakthrough hepatitis (BTH), defined as a flare of transaminases alanine aminotransferase (ALT),can occur during lamivudine monotherapy for hepatitis B virus (HBV) infection. There have been many reports of lamivudine resistant mutations within the C domain of the viral reverse transcriptase; however, the appearance of these mutants is not necessarily correlated with BTH during lamivudine therapy. Methods and Results. Entire serial HBV genomic sequences before and during lamivudine therapy for 4 patients with BTH and 1 patient without BTH were analyzed and showed changes in the pre S region. These changes may be associated with ALT flares. Further investigation in a cohort of 36 patients with a median treatment period of 25 months showed that 21 patients had a rise in HBV DNA titer, of whom 18 had BTH. Univariate statistical analyses showed that possible prognostic indicators for the occurrence of BTH were pre S deletions (P = 0.03) and L180M/M204L mutations (P = 0.04). By multivariate Cox regression analyses, significant variables were pre S deletions (hazard ratio, 0.17; 95%confidence internal (CI), 0.044-0.66) and precore mutations (hazard ratio, 5.70; 95%CI 1.74-18.71) prior to the commencement of lamivudine monotherapy. Interestingly, BTH occurred after the selection of the wild type species in the pre S region during lamivudine monotherapy. Conclusions. These results suggest that patients with HBV pre S deletionmutants should bemonitored carefully during lamivudine therapy. Background. Breakthrough hepatitis (BTH), defined as a flare of transaminases alanine aminotransferase (ALT), can occur during lamivudine monotherapy for hepatitis B virus (HBV) infection. There are been many reports of lamivudine resistant mutations within the C domain of the viral reverse transcriptase; however, the appearance of these mutants is not necessarily correlated with BTH during lamivudine therapy. Methods and Results. Entire serial HBV genomic sequences before and during lamivudine therapy for 4 patients with BTH and 1 patient without BTH were analyzed and showed changes in These changes may be associated with ALT flares. Further investigations in a cohort of 36 patients with a median treatment period of 25 months showed that 21 patients had a rise in HBV DNA titer, of whom 18 had BTH. Univariate statistical analyzes showed that possible prognostic indicators for the occurrence of BTH were pre-S deletions (P = 0.03) and L180M / M204L mutations (P = 0.04). By multivariate Cox regression analyzes, significant variables were preS deletions (hazard ratio, 0.17; 95% confidence internal (CI), 0.044-0.66) and precore mutations (hazard ratio, 5.70; 95% CI 1.74-18.71) prior to the commencement of lamivudine monotherapy. Interestingly, BTH occurred after the selection of the wild type species in the pre S region during lamivudine monotherapy. Conclusions. These results suggest that patients with HBV pre S deletion mutants should be monitored substantially during lamivudine therapy.