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Studying the most extreme outcomes of intergroup hatred – murder, mass killings and genocides – has long been part of historical and social research. Neuroscientists and psychologists have also been interested in interpersonal and intergroup violence. This article considers the question of how atrocities arise from a neuroscientific perspective, focusing on war as the context in which they most often occur. It describes relevant aspects of brain function, relates them to social psychological research on intergroup hostility and applies the resulting framework to a case study: the US prison camp at Guantanamo Bay.