OBJECTIVE: To assess and compare the association between household food insecurity and child nutritional status over two time-points taking into consideration the effects of a severe drought. DESIGN: The study used two cross-sectional household surveys during and after a severe drought, consistent with a natural experiment design. SETTING: The study took place in the district of iLembe, KwaZulu-Natal, South Africa. PARTICIPANTS: Households with children aged <5 years were invited to participate in the survey. Anthropometric measures were taken for the respective children in each of the participating households. RESULTS: The results indicated that all forms of poor nutritional status increased over the two time-points, with the most significant increases being for stunting (P < 0á016) and obesity (P < 0á001). There was evidence of an association between increasing food insecurity and stunting (P < 0á003) at the end of the drought, but not wasting, underweight or overweight. The results indicated a strong link between chronic food insecurity and chronic undernutrition. The results also showed stronger evidence of an association between food insecurity and stunting for urban households (P < 0á001) compared to their rural counterparts (P < 0á019). CONCLUSIONS: The negative effects of drought appear to contribute to increased rates of child stunting through higher levels of household food insecurity. Future research should assess this relationship through longitudinal studies. Interventions aimed at improving food security may assist in reducing child malnutrition, but policymakers should consider urban-rural differences as well as climatic and environmental events.