Research investigating the link between housing and health often produces mixed results. It does not always prove that good housing improves health. The results suggest a complex set of factors play a role, and the findings are sometimes contradictory. Two ways of addressing these concerns are longitudinal research, where the relationship between housing and health is measured in the short and medium terms, and a focus on children. We use the children’s housing and health data from the five waves of the National Income and Distribution Survey (NIDS) survey in South Africa, 2008 to 2017. We investigate the effect that continued living in informal housing over the five waves has had on these children’s health. Our results show a statistically significant relationship between prolonged residence in poor housing and poor health outcomes for some health indicators. The results call for a closer understanding of health issues in housing policy in South Africa.