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Despite years of interventions intended to reduce child malnutrition in South Africa, its negative effects, stunting in particular, persist mainly among children under five years old living in under-resourced regions. A cross-sectional study was conducted to determine the prevalence of malnutrition and associated factors among 404 children under age five attending childcare services with their mothers in selected healthcare facilities of Limpopo Province, South Africa. Anthropometry, socio-demographics and obstetric history were collected. Height-fo