Several observational studies provide evidence that acellular pertussis vaccines (aP) are less protective against pertussis disease than highly effective whole-cell pertussis vaccines (wP), however, concerns have been raised that some of these findings may be confounded by age. By undertaking age-stratified and restricted analyses on a cohort of Australian children primed with either aP-only, wP-only or mixed pertussis vaccine schedules, we demonstrate that compared to aP the association of wP with increased protection from pertussis is not confounded by age, nor by aP booster-dose receipt.