The proteomics era allows for the definition of biological organisms at the protein level, offering new opportunities for delimiting the self- and non-self boundaries between microbes and the human host. Here, we apply proteomics to design a vaccine against the major pathogenic factor of Campylobacter jejuni, i.e. cytolethal distending toxin (CDT). We used the scientific rationale that only peptide sequences not represented in the host proteome have the potential to evoke powerful, non-cross-reactive immune responses, thereby guaranteeing effectiveness and safety.