Epidemics may both contribute to and arise as a result of conflict. The effects of conflict on infectious diseases are complex and there have been confounding observations of both increase and decrease in disease outbreaks during and after conflicts. However there is no unified mathematical model that explains all these counter-intuitive observations. There is an urgent need for a quantitative framework for modelling conflicts and epidemics. We introduce a set of mathematical models to understand the role of conflicts inepidemics. Our mathematical framework has the potential to explain the counter-intuitive observations and the complex role of human conflicts in epidemics. Our work suggeststhat aid and peacekeeping organizations should take an integrated approach that combines public health measures, socioeconomic development, and peacekeeping in the conflictzone.Our approach exemplifies the role of non-linear thinking in complex systems like human societies. We view our work as a step towards a quantitative model of disease spread inconflicts.