Ground glass hepatocyte (GGH) represents a histological hallmark of chronic hepatitis B virus infection and contains surface antigens in the endoplasmic reticulum (ER). Several types of GGHs are recognized at different hepatitis B virus replicative stages. The recent identification of pre-S mutants from GGHs encourages us to investigate whether different GGHs may harbor specific mutants and exhibit differential biological activities. in this study, we applied laser capture microdissection to isolate specific GGHs from a total of 50 samples on eight resected liver specimens. The surface genes in two major types of GGHs were analyzed. Type I GGHs expressed an inclusion-like pattern of hepatitis B surface antigens and harbored mutants with deletions over pre-S1 region, whereas type H GGHs, distributed in clusters and emerged at late replicative phase, contained mutants with deletions over pre-S2 region that defines a cytotoxic T lymphocyte (CTL) immune epitope, and may represent an immune escape mutant. Transfection of pre-S mutants in Huh7 revealed decreased syntheses of middle and small S proteins with accumulation of large surface antigen in ER, which in turn led to the activation of ER stress response with differential activities for different mutants. This study therefore demonstrates that different GGHs may contain specific mutants and exhibit differential biological activities.