Politicians regard refugees increasingly as a security threat. Yet, systematic knowledge on the types, locations and frequency of security incidences involving refugees is limited. While existing conflict datasets include refugees as actors and refugee settlements as event locations, they do not provide more micro-level data on violent events involving refugees. This article introduces a novel subnational geo-coded dataset on refugee-related security incidences that records all instances of violence in Central and Eastern Africa between 1999–2010 that take place within refugee settlements or involve refugees, independently of where it happened. Using the new data, we show that most events are sexual and gender-based violent events and occur among refugees, while security incidences involving rebel groups occur relatively seldom. We demonstrate in an analysis at the administrative unit level that different types of refugee accommodations, camps and self-settlements, are both associated with refugee-related violence. Hence, stakeholders urgently need to upscale the protection of refugees at these locations, particularly in Kenya where most incidences were recorded.