In our previous studies on the development of synthetic peptide-based vaccines, we have evaluated flagellin from a Salmonella typhi vaccine strain as a carrier molecule for synthetic peptides derived from the influenza virus. The results indicated that the use of recombinant flagella, expressing defined influenza epitopes, is adequate for induction of protection against a challenge infection. It is of importance to show that previous exposure to the carrier does not induce suppression of the response to such vaccine. In the present study we demonstrate that the protective effect is not impaired by pre-immunization with either the carrier flagellin molecule alone or with the intact salmonella. The immune response was manifested both by the level of antibodies produced and by a proliferative cellular response, as well as by an efficient protection of the mice from a sub-lethal challenge infection. Since prior exposure to the carrier did not result in immune suppression, we conclude that Salmonella flagellin is a suitable carrier for synthetic peptide based vaccines.