Potential underestimation of the health system burden of pertussis was investigated by linking administrative datasets including pertussis notifications, hospitalizations and emergency department (ED) presentations for 1 304 876 children aged <15 years in NSW, Australia. From 2005 to 2008, 3006 children had a pertussis notification, 455 were hospitalized and 644 had an ED presentation with a coded diagnosis of pertussis. Linking hospital and ED records with pertussis notifications identified 140 hospitalizations and 735 ED presentations which occurred ± 7 days from notification but did not have a diagnosis of pertussis recorded. These additional events were more likely to have a diagnosis of bronchiolitis, upper respiratory infection and cough compared to all other admissions and presentations. Including these additional events significantly increased the proportion of notified cases that were hospitalized or visited EDs, particularly for those aged 5 to <15 years. Linked administrative data allowed more comprehensive estimation of the health system burden of pertussis.