Conflict, displacement, food insecurity and poverty make affected populations more vulnerable to HIV transmission. However, the common assumption that this vulnerability necessarily translates into more HIV infections and consequently fuels the HIV/AIDS epidemic is not supported by data. Whether or not conflict and displacement affect HIV transmission depends upon numerous competing and interacting factors. This paper explores and explains the epidemiology of HIV/AIDS in conflict and addresses the unique characteristics that must be addressed when planning and implementing HIV/AIDS interventions among populations affected by conflict as compared with those in resource-poor settings. These include targeting at-risk groups, protection, programming strategies, coordination and integration and monitoring and evaluation. Areas for future HIV/AIDS operational research in conflict are discussed.