This paper measures and decomposes socio-economic inequality in childhood malnutrition in Nigeria. Individual data records were constructed for a nationally representative sample of 4187 under-5 children. The data were taken from the Nigerian Demographic and Health Survey in 2003. The household's socio-economic status was measured using principal component analysis. The concentration index of childhood malnutrition was used as a measure of socio-economic inequality and decomposed into its determining factors. The largest contributions to inequality in childhood malnutrition were household economic status (31%), health service index (17%), maternal education (13%) and proper sanitation (11%). Breastfeeding duration (8%), geopolitical regions (8%) and residency in rural/urban areas (5%) also proved important contributors to the measured inequality. The findings indicate that socio-economic inequality in childhood malnutrition in Nigeria is determined not only by health system functions, but also by factors beyond the scope of health authorities and care delivery system. Scaling up universal approach linking the Ministry of Health and Ministry of Education with other ministries may speed up the reduction of inequalities in social determinants of childhood malnutrition.