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The new millennium brought renewed attention to improving the health of women and children. In this same period, direct deaths from conflicts have declined worldwide, but civilian deaths associated with conflicts have increased. Nigeria is among the most conflict-prone countries in sub-Saharan Africa, especially recently with the Boko Haram insurgency in the north. This paper uses two data sources, the 2013 Demographic and Health Survey for Nigeria and the Social Conflict Analysis Database, linked by geocode, to study the effect of these conflicts on child health. We show a strong association between living close to a conflict zone and acute malnutrition in Nigerian children in 2013. This is related to the severity of the conflict, measured both in terms of the number of conflict deaths and the length of time the child was exposed to conflict. The association with mortality is much less clear, with essentially no significant relationship to conflict detected using these data for the period studied. Undoubtedly civil conflict is limiting the future prospects of Nigerian children and the country’s economic growth. In Nigeria conflicts in the north are expected to continue with sporadic attacks and continued damaged infrastructure. Thus, the children in Nigeria will continue to suffer the consequences documented in this study.