Pertussis has a worldwide incidence of 51,000,000 cases per year with a 1% case fatality rate and primarily affects young children. Despite the availability of an effective whole-cell pertussis vaccine, pertussis has reemerged as a significant cause of human morbidity in areas where pertussis vaccine programs have ceased because of vaccine safety concerns. The search for new vaccines without side effects has stimulated an intensive study of virulence determinants of Bordetella pertussis. As a result of this research, virulence genes of B pertussis and factors that regulate these genes have been identified and characterized. The molecular characterization of the virulence determinants of B pertussis has helped to elucidate the basis of some of the clinical observations that characterize disease caused by B pertussis. It appears that host factors may potentially determine whether virulence genes are expressed. It is now possible to construct mutants of B pertussis that are deficient in individual virulence determinants. The era of the molecular Koch's postulates is upon us, and the roles of individual virulence factors in disease pathogenesis can be studied. In this article, issues concerning immunity to pertussis, safety of whole-cell vaccine, and virulence factors of B pertussis are considered. The molecular Koch's postulates as they relate to testing prospective virulence factors in pertussis infection model systems will be presented. The mucosal environment as a potential modulator of virulence factors will be addressed.