Sub-Saharan Africa disproportionately represents the largest incidence of both HIV/AIDS and internal conflicts. The impact of conflict on HIV incidence is largely unknown. Current epidemiological evidence paradoxically suggests that in most populations affected by conflict, HIV prevalence is lower than surrounding communities. However, in situations of conflict, the most vulnerable populations, such as women and children, are at increased risk for HIV through sexual violence, forced occupational exposure and an absence of access to health care or testing. Together, these dimensions of conflict create a complex and challenging situation for prevention of HIV/AIDS and delivery of care to conflict-affected populations. We examine the complexity of monitoring HIV/AIDS in conflict settings. We argue that increased efforts are needed to protect vulnerable populations and design health-delivery systems that are sustainable in settings of conflict.