Pertussis is an acute, communicable infection of the respiratory tract caused by Bordetella pertussis and occasionally by B. Parapertussis which is spread by droplets from person to person. There are an estimated 50 million cases of pertussis and 300 000 pertussis-related deaths per annum globally mostly in unimmunised or incompletely immunised infants, who have more severe disease and are more likely to have complications. At present there is no active surveillance system or reliable clinical case definition of pertussis leading to a substantial underestimate of the true prevalence of disease in South Africa. Polymerase chain reaction (PCR) testing on nasopharyngeal aspirates and sputum specimens has greatly improved the ability to confirm pertussis cases but currently there are only two public health laboratories that offer this test in South Africa. By performing PCR testing for Bordetella pertussis and Parapertussis on nasopharyngeal aspirates of infants admitted to Red Cross Hospital, presenting with respiratory symptoms, the prevalence of disease (and carrier status of the mothers of the children who test positive) can be estimated. The type of viral respiratory co-infection in children as well as potential risk factors (ie age, HIV status, smoke exposure and lack of immunisation) will also be demonstrated.