Human health in our cities is an expression of complex social and environmental interactions not previously faced in our long evolutionary history. In this paper, we present a social–ecological perspective on the complex nature of emerging public health problems in cities and identify some of the research questions emerging from this new view of the city. We argue that an integrative urban science agenda is needed not only to inform urban policy, planning and design, but also to alert people to the consequences of and trade-offs around their choices and behaviours.