Sunetra Gupta and Roy Anderson discuss how the balance between host immune responses against conserved and variable antigens shapes the population structure of pathogens. At one extreme, immune selection against polymorphic determinants can cause pathogen populations to self-organize spontaneously into discrete antigenic types that may either be maintained over long periods or undergo cyclical or chaotic fluctuations. At the other extreme, diversity may be drastically reduced by competition induced by a strong immune response against a conserved determinant. Where does each pathogen lie along this continuum? How would this knowledge influence our attempts to control an infectious disease?