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Pertussis vaccines have been effective at reducing pertussis-associated morbidity and mortality. However, they have a complex array of limitations, particularly associated with the duration of protection against clinical disease and imperfect immunity (carriage and transmission). Little is known about risk factors for pertussis vaccination failure. Understanding pertussis vaccination failure risk is most important in the paediatric population. This study aims to investigate risk factors for pertussis vaccination failure in (1) infants between birth and six weeks of age born to mothers who received pertussis booster vaccinations during pregnancy and (2) infants after the completion of the primary series (approximately five months old) to four years old. This will be achieved in a two-step process for each study group. Pertussis vaccination failure cases will first be described using a case series study design, relevant case characteristics will be sourced from six national administrative datasets. The case series study results will help select candidate risk factors (hypothesis generating step) to be tested in the retrospective cohort study (hypothesis testing step). Pattern analysis will be used to investigate risk factor patterns in the cohort study. The identification of higher risk groups enables targeting strategies, such as additional doses, to better prevent pertussis disease.