Issues around health equity in conflict-affected fragile states have received very little analysis to date. This paper examines the main factors that threaten health equity, the populations that are most vulnerable and potential strategies to improve health equity. The methods employed are a review of the published and grey literature, key informant interviews and an analysis of data on social determinants of health indicators. A new conceptual framework was developed outlining types of inequity, factors that influence equity and possible strategies to strengthen equity. Factors that affect equity include displacement, gender and financial barriers. Strategies to strengthen health equity include strengthening pro-equity policy and planning functions; building provider capacity to provide health services; and reducing access and participation barriers for excluded groups. In conclusion, conflict is a key social determinant of health. More data is needed to determine how conflict affects within-country and between-country equity, and better evaluated strategies are needed to reduce inequity.