The genus Bordetella contains several pathogenic species generally associated with upper respiratory tract infections in warm-blooded animals. Bordetella pertussis is the etiologic agent of whooping cough. Whooping cough is presently one of the ten most common causes of death from infectious diseases and reported by the World Health Organisation (WHO) to cause 50 million cases and 350000 deaths worldwide per year, mainly among unvaccinated individuals in poor countries. The term proteome, in analogy to the term genome, was coined to describe the complete set of proteins that an organism has produced under a defined set of conditions. Proteomics has been used to identify novel bacterial vaccine candidates against several human pathogens. Fueled by growing DNA sequence information, the analysis of the proteome becomes a valuable and useful tool for antigen discovery. Much of information about immunogenic component can be derived from proteomics coupled to Western blotting, namely immunoproteomics. v In the present study, we report first immunoproteomics analysis to identify candidate antigens of B. pertussis for vaccine development. Different sera from mice, which were immunized or challenged with B. pertussis, were analyzed for reactivity by Western blot against whole cell extracts of B. pertussis Tohama and Saadet strains separated by 2-DE. We identified 15 immunogenic proteins of Bordetella pertussis as a total (60 kDa chaperonin, heat shock protein, serum resistance protein, putative substrate-CoA ligase, ATP-dependent protease, preprotein translocase secA subunit, S-adenosylmethionine synthetase, elongation factor Tu, RNA polymerase alpha subunit, ketol-acid reductoisomerase, pertactin, lysyl-tRNA synthetase, serum resistance protein, carbamoyl-phosphate synthase large chain, 30S ribosomal protein S1 subunit), 6 of which being identified as immunogenic in a pathogenic microbe (ATP-dependent protease, carbamoylphosphate synthase large chain, lysyl-tRNA synthetase, putative chromosome partition protein, preprotein translocase secA subunit, 30S ribosomal protein S1 subunit) and 5 identified as immunogenic for Bordetella pertussis (RNA polymerase alpha subunit, S-adenosylmethionine synthatase, putative substrate-CoA ligase, elongation factor Tu, ketol-acid reductoisomerase) for the first time.