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Using the archives of the Commission nationale de lutte contre le génocide (National Commission for the Fight Against Genocide, CNLG), the organization tasked with memorializing the Rwandan genocide, this article seeks to understand the controversy, between 1994 and 2003, over the patrimonialization of churches that were genocide sites. This article focuses on three particular dimensions. Firstly, it analyzes the theological debate over purifying churches where massacres took place during the genocide. It then examines the political negotiations between the Rwandan state and the Catholic Church over these churches’ historical legacy. Finally, it discusses the geopolitical dimension of these debates and the influence of the Vatican. The author concludes by looking at the current national and international controversies over these sites.