Bordetella pertussis is the causative agent of whooping cough ( pertussis) which is a worldwide vaccine preventable acute respiratory illness that predominantly involves infants. The reactogenicity of whole-cell (Pw) vaccines and the difficulty of their consistent production have led to the development of acellular pertussis (Pa) vaccines. However, despite high vaccination coverage using either Pw or Pa and introduction of adolescent and adult vaccines with reduced antigen content, there are still reports about the circulation of the microorganism in populations, morbidity in infants and increasing incidence of pertussis among adolescent and adults who transmit the infection to yet unimmunized infants. Waning vaccine-induced immunity and antigenic divergence in circulating strains seem to be the major problems accounting for resurgence of pertussis. Considering the need for new vaccination strategies, improvement of current Pa vaccines by including new virulence factors would probably be the most rationale strategy. Recent advances in B. pertussis proteomics, subproteomics and immunoproteomics greatly aided in identifying novel antigens of the pathogen. Future studies involving quantitative transcriptomic and proteomic profiling of host-B. pertussis interactions, studying gene expression in vivo and reverse vaccinology will also be very promising approaches and tools to develop pertussis vaccines inducing long term immunity.