Early life vaccination is necessary to protect young children from dental caries. Our group had previously reported that a plasmid DNA vaccine pGJA-P/VAX against the glucosyltransferase (GTF) enzyme and cell surface antigen AgI/II (PAc) of Streptococcus mutans (S. mutans) elicited a specific and protective immunity in adult experimental animal models. In this report, early life immunization with the same plasmid was studied following intranasal (i.n.) and intramuscular (i.m.) delivery in murine models. The potential of inducing mucosal and systemic immune responses to special antigens was measured by ELISA. In addition, cytokine production and protection effectiveness against dental caries formation were also investigated. In the i.n. route, rats were primed when they were 5 days old, and boosted after 10 and 20 days with either plasmid pGJA-P/VAX-bupivacaine complexes, or pGJA-P/VAX alone, or empty vector. The pGJA-P/VAX-bupivacaine combination was able to mount the immune responses characterized by increased antibody levels of specific salivary IgA and serum IgG, preferential IFN-gamma production and significant reduction in the dental caries lesions. In the i.m. route, rats were vaccinated with either pGJA-P/VAX alone or empty vector with the same immunization schedule as the i.n. route. Plasmid pGJA-P/VAX alone induced a significant increase in the serum IgG and IFN-gamma production. However, it was not effective in eliciting specific salivary IgA and in decreasing the dental caries formation. All these findings indicate the feasibility of immunity with a targeted fusion DNA vaccine to a young immune system.