An important issue in the dynamics of directly transmitted microparasites is the relationship between infection probability and host density. We use models and extensive spatio-temporal data for the incidence of measles to examine evidence for spatial heterogeneity in transmission probability, in terms of urban–rural hierarchies in infection rate. Pre-vaccination measles data for England and Wales show strong evidence for urban–rural heterogeneities in infection rate – the proportion of urban cases rises significantly before major epidemics. The model shows that this effect is consistent with a higher infection rate in large cities, though small towns have epidemic characteristics intermediate between town and country. Surprisingly, urban and rural areas of the same population size have a similar propensity for local extinction of infection. A spatial map of urban–rural correlations reveals complex regional patterns of synchronization of towns and cities. The hierarchical heterogeneities in infection persist into the vaccine era; their implications for disease persistence and control are discussed.