Previous research has shown that conflict is associated with the spread of diseases and the destruction of a country’s public health infrastructure. This work complements this field of research by providing a novel and systematic investigation of the role disease environments play as a determinant of civil conflict. This analysis uses a novel measure of the presence of deadly multi-host vector-specific transmitted diseases in a country to build an innovative dataset to conduct within-country variation analysis over time to provide a statistically strong and qualitatively relevant robust analysis that documents epidemics are a direct channel for civil conflict.