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The war also killed a significant number of civilians; battles raged across farm and field, encampments of troops spread epidemic disease, guerrillas ensnared women and children in violence and reprisals, draft rioters targeted innocent citizens, and shortages of food in parts of the South brought starvation. No one sought to document these deaths systematically, and no one has devised a method of undertaking a retrospective count. The distinguished Civil War historian James McPherson has estimated that there were 50,000 civilian deaths during the war, and has concluded that the overall mortality rate for the South exceeded that of any country in World War I and all but the region between the Rhine and the Volga in World War II.

https://www.nps.gov/nr/travel/national_cemeteries/death.html