Economic inequality has been hypothesized to be a determinant of population health, independent of poverty and household income. We examined the association between economic inequality and child malnutrition in Ecuador. Economic inequality was measured by the Gini coefficient of household per capita consumption, estimated from the 1990 Census. Childhood stunting, assessed from height-for-age z scores, was obtained from the 1998 Living Standards Measurement Survey (LSMS). We controlled for a range of individual and household covariates, including per capita food consumption, education, housing, ethnicity, fertility, access to health services, diarrhea morbidity, child care, mother's age and diet composition. Stunting still affects 26% of children under five in Ecuador, with higher prevalence in the rural Highlands and among indigenous peoples. Maternal education, basic housing conditions, access to health services, ethnicity, fertility, maternal age and diet composition were independently associated with stunting. However, after controlling for relevant covariates, economic inequality at the provincial scale had a statistically significant deleterious effect on stunting. At municipal or local levels, inequality was not associated with stunting.