During the genocide in Rwanda in 1994, Gregoire Ndahimana held the position of Bourgmestre of Kivumu in Kibuye préfecture. In this position he exercised authority over his subordinates, including wanted genocide suspect, Fulgence Kayishema.
For his alleged role in the genocide, Gregoire Ndahimana is charged with genocide or complicity in the alternative, conspiracy to commit genocide, and extermination as a crime against humanity. According to the indictment, dated 5 July 2001, Ndahimana is individually responsible and responsible as a superior for various crimes, including the Nyange Parish massacre in which more than 2,000 Tutsi refugees were slaughtered. Ndahimana is said to bear responsibility alongside convicted génocidaire and former priest, Athanase Seromba for this incident, in which Tutsis encouraged by Ndahimana to gather at the parish for their ‘safety’ were subsequently killed en masse.
Gregoire Ndahimana was arrested on 11 August 2009 by Congolese armed forces in the North Kivu Province of eastern Democratic Republic of the Congo (DRC). Ndahimana was arrested during joint Rwanda-DRC operations against the Democratic Forces for the Liberation of Rwanda (FDLR) Hutu rebels thought to consist of many of the remaining Interahamwe militias and génocidaires from 1994. Ndahimana was transferred to the custody of the Tribunal on 20 September 2009 and pleaded not guilty at his initial appearance eight days later.
The trial of Ndahimana commenced on 6 September 2010 in Trial Chamber III at the International Criminal Tribunal for Rwanda.