Whooping cough and diphtheria are vaccine preventable diseases. Diphtheria, due to Corynebacterium diphtheriae or Corynebactium ulcerans, two Gram positive bacteria, is a serious upper respiratory tract disease with high morbidity and mortality rates. Vaccination, via an acellular vaccine composed only of purified, detoxified diphtheria toxin, has significantly reduced the incidence of the disease in most of the developed world. However, the lower vaccine coverage of diphtheria vaccination in adults is now a cause for concern. Furthermore, the disease remains endemic in many developing countries where the vaccine coverage is low. Whooping cough, due to Bordetella pertussis or Bordetella parapertussis, two Gram negative bacteria, is a severe and highly contagious respiratory disease. The use of pertussis whole cell vaccines, containing inactivated bacteria, or later on pertussis acellular vaccines, only containing one to five purified, detoxified bacterial proteins, reduced dramatically the incidence of the morbidity and mortality. However, despite a high coverage the disease is still endemic in many regions of the world. Explaining this epidemiologic situation is, however, difficult since pertussis, vaccines, strategies, coverage, awareness of the disease and surveillance systems differ around the world. It is thus urgent to establish reference laboratories around the world using standardized clinical diagnosis and specific and sensitive diagnostic methods.