This paper uses multilevel modelling and Demographic and Health Survey data from five African countries to investigate the relative contributions of compositional and contextual effects of socioeconomic status and place of residence in perpetuating differences in the prevalence of malnutrition among children in Africa. It finds that community clustering of childhood malnutrition is accounted for by contextual effects over and above likely compositional effects, that urban–rural differentials are mainly explained by the socioeconomic status of communities and households, that childhood malnutrition occurs more frequently among children from poorer households and/or poorer communities and that living in deprived communities has an independent effect in some instances. This study also reveals that socioeconomic inequalities in childhood malnutrition are more pronounced in urban centres than in rural areas.