As part of development of a component vaccine against dental caries, the catalytic region (CAT) and glucan-binding domain (GBD) of glucosyltransferase B (GtfB) from Streptococcus mutans have been employed as target antigens, because they theoretically include epitopes associated with enzyme function. However, their antigenicity has not been fully evaluated. Although there are many reports of successful vaccinations performed with these components, the principle has not yet to be put into practical use. Thus, we have come to doubt their antigenicity and reevaluated the antigenic region of GtfB using in silico analyses in experiments conducted in vitro and in vivo. Our results suggest that the variable region (VR) in the N-terminus of GtfB is immunodominant and S. mutans and/or GtfB specific, while it is not conserved in other streptococcal Gtfs and has an unknown function. Successful immunization with an adenovirus-vector borne DNA vaccine confirmed that VR is a useful epitope that shows promise for development of a caries vaccine.