This paper models how migration both influences and responds to differences in disease prevalence between cities and shows how the possibility of migration away from high-prevalence areas affects long-run steady state disease prevalence. We develop a dynamic framework where migration responds to the prevalence of disease, to the costs of migration and to the costs of living. The model explores how pressure for migration in response to differing equilibrium levels of disease prevalence generates differences in city characteristics such as land rents. Competition for scarce housing in low-prevalence areas can create segregation, with disease concentrated in high-prevalence “sinks”. We show that policies affecting migration costs affect the steady-state disease prevalence across cities. In particular, migration can reduce steady-state disease incidence in low-prevalence areas while having no impact on prevalence in high-prevalence areas. This suggests that, in some circumstances, public health measures may need to avoid discouraging migration away from high-disease areas.