Background: Amino acid (AA) changes in specific hepatitis B core antigen (HBcAg) regions were assessed in patients infected with chronic hepatitis B (CHB) after a 12-month untreated period and after receiving antiviral therapy (interferon, lamivudine or adefovir dipivoxil), and in inactive hepatitis B surface antigen-positive carriers. Methods: Samples corresponding to different time points in 76 CHB cases (64 on-treatment) and 4 inactive carriers were included. The main precore mutation, T-helper immunodominant epitope at AA 50-69 (Th50-69), minor T-helper epitope (Th28-47), B-cell immunodominant epitope (B74-84) and a conserved region of HBcAg at AA 1-11 (AA1-11) were directly sequenced. For comparisons, the average number of AA changes in each region was standardized to 12 months (Av12). Results: AA changes clustered mainly in immunodominant regions (69%). The highest percentage of cases (%n) with changes and highest Av12 changes were detected after interferon treatment (%n=73%, Av12=3.1 in Th50-69 and %n=86%, Av12=2.7 in B74-84). At baseline, immunodominant regions had higher Av12 changes in hepatitis B e antigen-negative patients and those with main precore mutations. Changes in the Th28-47 region were more frequent after nucleoside/nucleotide analogue treatment (40%) than before treatment (9%). Codons 74 and 77 were the most polymorphic, and the double change E64D-N67T was significantly observed. Codon 84 substitutions were mainly associated with interferon treatment (P=0.05). Conclusions: Natural and treatment-induced substitutions in HBV core protein, occurring especially with interferon treatment, were characterized. Some immune-stimulating activity related to the minor Th28-47 epitope might be associated with nucleoside/nucleotide analogues; this activity was also seen in inactive carriers. ©2011 International Medical Press.