This paper studies the relationship between civil war and HIV/AIDS in Burundi at the micro level. The case of Burundi provides interesting grounds of analysis, as seroprevalence rates are heterogeneous across the country, the serological and conflict data for Burundi are of good quality and conclusions can inform HIV/AIDS policies in Burundi and other fragile states. Ordinary least squares and instrumental variable results indicate that there is no empirical relationship between seroprevalence at the general population level and three measures of local conflict intensity within provinces. This evidence could imply that areas that are relatively more conflict affected do not need to be prioritized over others in terms of HIV/AIDS policies. Further research should focus on individual rather than geographical exposure to conflict. There are likely certain groups and individuals at risk in the general population that need special attention after conflict. Furthermore, violence changes societies, in particular gender relations, thereby indirectly feeding and possibly fueling the dynamics of the epidemic.