The flagellum of Campylobacter jejuni is not only responsible for initiating colonization of the gastrointestinal tract of host animals but is also a major antigen that induces protective immune responses. However, protection is limited to the homologous strain and the ability to protect against multiple serotypes has yet to be determined. In this study, we have shown that FlaA is an immunodominant protein on NCTC11168 CJ1 flagella and we mapped the immunoreactive epitopes on the protein by probing a series of overlapping synthetic peptides spanning the entire sequence with sera against multiple C. jejuni serotypes. Amino acid residues 176-205 (P8), 376-405 (P16) and 501-530 (P21) were immunodominant and cross-reactive. The mucosal IgA in the intestinal secretions of CJ1-infected birds reacted significantly with peptides P16 and P21 indicating that the specificity of the mucosal response is different from the systemic response. Antisera raised against formalin-killed CJ1 cells and purified flagellin showed positive reactivity with a subset of peptides identified by antisera against live C. jejuni. This study provides insight into the specificity of the host immune responses to the FlaA protein of C. jejuni and suggests that these sequences merit further testing for their immunogenicity and potential as subunit vaccine candidates for multiple serotypes.