Understanding the causes and consequences of conflicts continues to be an important contribution to the economic development literature, particularly the mechanisms that can reduce civilian deaths. We contribute to understanding attacks on civilians and the spillover effects by analysing the impact of government religious preference on civilian deaths. Using panel data analysis for 113 countries for the period 1989 to 2015, we find that a higher government preference towards religion causes more civilian deaths for countries experiencing intrastate conflict. Furthermore, we analyse this effect by the different types of conflict and find that the results are driven by both state-based and non-state-based conflicts. Lastly, a regional analysis shows that the negative impact of a strong preference towards religion from the government is particularly notable for countries in Africa and Asia.