Background: Stunting continues to affect young children as a global nutritional disorder. The aim of our study was to assess the prevalence, associated risk factors and spatial clustering for stunting in a disadvantaged South African District. Methods: A community-based cross-sectional weighted survey of households was conducted in the iLembe district, KwaZulu-Natal in 2014. Children aged 0-59 months were included in the study sample. Height for age Z scores were calculated for the children and the spatial clustering was assessed. Results: Of the 572 children included in the weighted analyses, 21.1% (95% confidence intervals (CI) 18.0-24.5) were classified as stunted and of these 7.5% (95% CI 5.3-10.4) were severely stunted. Conclusion: Stunting is a major public health burden in SA that requires intervention at a community level. A multi-sectoral approach is required to reduce stunting prevalence, focusing on child growth and development monitoring, nutrition education and household food security.