HBeAg seroconversion in HBV patients is considered an important event. We determined precore (PC) and base core promoter (BCP) mutations in 137 HBeAg-positive nucleos(t)ide analogues (NA) treated patients by INNO-LiPA HBV PreCore assay (Innogenetics). The majority of patients with nongenotype A had PC/BCP mutants present at baseline (P=0.02). During 29months of therapy, 45 patients achieved HBeAg seroconversion. Probability of HBeAg seroconversion was higher in patients with PC and/or BCP mutants (P=0.01). After HBeAg seroconversion, patients with BCP mutants had more HBeAg relapse (P=0.07), and PC mutants less often achieved HBV DNA<2000IU/mL (P=0.07).