We have previously shown that gene-gun delivery of murine rotavirus DNA vaccines to the epidermis induced protection against rotavirus challenge in mice. In this study, we used a rotavirus group antigen (VP6)-specific DNA vaccine to compare epidermal immunization with immunization to the anorectal epithelium for efficacy in inducing protective immunity. The vaccine was administered into cells of the abdominal epidermis or anorectal epithelium of adult BALB/c mice with an Accell gene-gun (PowderJect, Inc). Vaccines administered by either route elicited rotavirus-specific ELISA antibodies and analysis of the IgG subtypes indicated Th2-type responses were generated by both routes of administration, in contrast to Th1-type responses generated by live rotavirus. Protection against virus challenge was obtained in mice inoculated by either route, as shown by significant reduction of virus excreted in stools. The protection obtained by immunization of the anorectal epithelium was greater than that for epidermal immunization at the same vaccine dose. These results suggest that mucosal immunization of DNA vaccines may be an effective means to generate protective immunity against mucosal pathogens.