An understanding of the consequences of infection and vaccination on host immunity sets the stage for interpreting pertussis epidemiology. Yet, with no known serological marker of protection, such an understanding is currently not possible. Here, we interrogate longitudinal age-stratified pertussis incidence reports from Sweden and Massachusetts, USA, with the aim of quantifying the impact of infection and immunization on protective immunity. Our analysis of Sweden data during the vaccination hiatus period (1986–1996) indicates that adults contribute little to transmission. This may be either because infection-derived immunity is very long-lasting, or that individuals whose immunity has waned are subsequently less susceptible. The analyses of Massachusetts data (from 1990–2005) identify the primary mechanism of vaccine failure—for both whole cell and acellular—to be waning. However, the average duration of immunity is identified as many decades, though our model predicts substantial individual variability in this trait. Finally, we demonstrate our estimates to be consistent with those obtained from popular measures of vaccine effectiveness, though our interpretation of these findings is quite different.