Geographic factors such as rugged terrain and distance from capital cities are widely believed to prolong civil wars by enabling rebel groups to resist total defeat. This article argues that prevalence of malaria can similarly serve to asymmetrically enhance rebels’ defensive capabilities and thus prolong civil war. Malaria prevalence does so in three complementary ways. First, while malaria can inflict costs on both government and rebel troops, these costs are magnified for larger and denser human groups; thereby ensuring that the costs of malaria will often be higher among government troop deployments. Second, because government soldiers are rotated in and out of conflict zones whereas insurgents typically are not, the former are likely to have a higher nonimmune exposure rate than the latter, which further ensures that government forces will be more susceptible to contracting and spreading malaria. Third, malaria can also indirectly prolong civil war by helping to maintain a socio-geographic environment that is conducive to insurgency. These three complementary factors advantage rebel forces’ abilities to resist defeat by government forces and prolong civil conflicts. I empirically test these arguments by examining the duration of civil wars and find strong support for a prolonging effect of malaria on civil conflict.