This study determined the socio-demographic, nutritional and health status of children and their caregivers in two rural districts in KwaZulu-Natal (KZN) and one rural district in the Eastern Cape (EC), South Africa. Design: A cross-sectional survey was conducted. Setting: The study population resided in Umkhanyakude (sub-district Jozini) and Zululand (sub-district Pongola) in KZN, and in OR Tambo (sub-district Nyandeni) in the EC province. Subjects: Children 0 to 59 months old (Umkhanyakude n = 398; Zululand n = 303; OR Tambo n = 364) and their caregivers were included. Methods: Structured interviewer-administered questionnaires were conducted and height and weight were measured. Results: Households in OR Tambo had less access to services (tap water 3%, toilets 33%), compared to Umkhanyakude (tap water 50%, toilets 82%) and Zululand (tap water 74%, toilets 98%). Wood was the main energy source used to cook food in all three districts (> 75%). Grants were a main source of income (Umkhanyakude and Zululand 61%; OR Tambo 55%). Many households obtained vegetables from their own garden (Umkhanyakude and Zululand 30%; OR Tambo 70%). The households that reportedly had enough food available at all times (Umkhanyakude and Zululand 25%; OR Tambo 17%), were in the minority. The diarrhoea prevalence reported by the caregivers was high (Umkhanyakude 35%; Zululand 24%; OR Tambo 24%). The prevalence of stunting was higher for children older than 12 months and varied between 22 and 26%. The prevalence of overweight among children 0 to 23 months exceeded the prevalence of underweight. The prevalence of overweight and obesity among caregivers was high (Umkhanyakude 42%; Zululand 60%; OR Tambo 56%). Conclusion: Concerted efforts are needed to address the adverse social, nutrition and health conditions in these districts.