In Rwanda, following the 1994 Genocide against the Tutsi, many people were found guilty of genocide crimes and imprisoned. Their children ended up in a situation of ambiguous loss during and after a parent’s imprisonment. The article presents the multidimensional impact of this loss on the everyday lives of these children and their families according to key themes as they emerged from an ethnographic study in which 21 children and their family members participated. Themes include changed family dynamics and family stress, economic deprivation, incomprehension of a parent’s criminal past, the social stigma of being a child of a génocidaire, and strategies used to make the loss bearable. The uniqueness of the ambiguous loss as experienced by children of perpetrators of genocide in Rwanda compared to those of perpetrators of the Holocaust or other mass crimes relates to an amalgam of factors specific for the context of post-genocide Rwanda; major ones being the severity of genocidal crimes and gacaca courts Rwanda chose as its main form of transitional justice. The case study illustrates how using the prism of intergenerational relations helps to understand some of the transformative and enduring effects of a crisis that deeply affects a society.