Hepatitis B (HB) is a worldwide public health problem, closely related with liver cirrhosis and hepatocellular carcinoma (HCC). The implementation of universal hepatitis B virus (HBV) vaccination programs has led to significant reduction in incidence of acute and chronic HB, liver cirrhosis and HCC. However, this success is now being threatened by the discovery of HBV vaccine breakthrough infection caused by the S gene mutants of HBV, high maternal viral load and virus-induced immunosuppression. An alteration in the antigenicity and immunogenicity of hepatitis B surface antigen (HBsAg) due to S gene mutations may compromise detection of HBsAg (diagnosis-escape mutants), treatment with hepatitis B-specific immunoglobulin (HBIG), and even cause infections in individuals who are antihepatitis B surface antigen (anti-HBs) antibody-positive after immunization (vaccine-escape mutants). By surveilling for S gene mutants of HBV among vaccinated population, we will have a better understanding of the mechanism of HBV vaccine breakthrough infection; potentially providing new ideas for designing better diagnostic assays and effective vaccines for prevention and treatment of HBV. This review attempts to briefly summarize the status and role of S gene mutations, B-cell epitopes and T-cell epitope mutants, and surveillance of mutant HBV variants in a hospital setting.