Host immunity is a strong selective force on pathogen populations, and systematic differences in their interactions with the immune system partly explain pathogens’ divergent epidemiological and evolutionary patterns. A common assumption is that pathogens typified by multiple strains undergo some kind of negative frequency dependent selection by the adaptive immune response, leading to rapid strain turnover or the coexistence of minimally overlapping strain sets. In this talk, I describe how this conception is incomplete for several common pathogens. Sexually transmitted types of human papillomavirus, which infect over 40% of adults in the United States, in fact show close to neutral dynamics. Influenza, which infects approximately one-fifth of people each year, experiences competing selective pressures in different host subpopulations. Importantly, vaccination changes not only the strength but also the type of immune-mediated selection on each pathogen. A richer immunological context for the ecological and evolutionary dynamics of both human papillomavirus and influenza suggests that vaccines against each may be more effective than currently appreciated.