Pertussis or whooping cough is a highly contagious community disease mainly caused by Bordetella pertussis and B. parapertussis. We report a minor outbreak of whooping cough (2009–2010) in symptomatic subjects from Bisham, near Swat, Khyber Pukhtoonkhawa province, Pakistan. Interestingly, our results show that all the culture-positive isolates (n = 21) collected from children (average age 3·46 years), were identified as B. parapertussis after routine identification tests and PCR IS481, IS1001 and IS1002. Furthermore, in the affected patients, none had received immunization with diphtheria-pertussis-tetanus (DTPw) vaccine. Therefore, the possibility of the re-emergence of the disease due to limitation of basic health services as a result of the political unrest due to the 9/11 situation is also examined. Moreover, we discuss the importance of vaccinating both adults and children with DTPwPaw vaccine containing both organisms for better protection.