Electroporation (EP)-mediated DNA immunization can elicit effective immune responses in a variety of animals, and is widely used in research studies and clinical trials. However, high-pulse voltage, high DNA dose and multiple immunizations are still required to achieve considerable immune responses. To further improve the efficiency of EP-mediated DNA immunization, many parameters have been tried and optimized in recent years. In our early research, we found that the short noncoding DNA fragments (sf-DNA) can significantly enhance EP-mediated transgene expression of reporter genes. In this study, we tested the effect of sf-DNA on the immune potency of EP-mediated hepatitis B virus (HBV) DNA vaccination in a mouse model. The results show that the use of sf-DNA in EP-mediated HBV DNA vaccination leads to an enhanced expression of the HBV surface antigen, resulting in higher cellular and humoral responses. Furthermore, the immune responses in the sf-DNA-mediated 120 V cm(-1) EP immunization group were higher than that of the 200 V cm(-1) EP without sf-DNA groups. These data suggest that the sf-DNA can be used as an effective helper molecule to improve the immune response of EP-mediated HBV DNA vaccination, which may make the EP-mediated DNA vaccination more effective and suitable for animal and clinical application.