The present article offers a historical overview on pertussis (whooping cough) by analysing the ancient epidemic manifestations of the disease and the path towards the discovery of an effective vaccine against it. The original mentions of pertussis are examined with reference to Mediaeval Afghanistan and the famous AD 1578 Paris epidemic described by the French physician Guillaume de Baillou. The historical data are then matched with information derived from analyses of phylogenetic trees of B. pertussis. Finally, this article also highlights some recent challenges posed to public health by this infectious disease.