On 2 August 2001, Grégoire Ndahiman was charged by the Prosecutor of the International Criminal Tribunal for Rwanda with genocide, or in the alternative, complicity in genocide, conspiracy to commit genocide and crimes against humanity for extermination.
He remained at large until 11 August 2009, when he was arrested in a village in Congo's North Kivu province. The arrest was the result of a joint Rwandan-Congolese military operation which took place five days after a summit meeting, on 6 August, in Goma, between the presidents of the Democratic Republic of the Congo and Rwanda.
Grégoire Ndahimana was transfered to the ICTR on 20 September 2009.
His initial appearance before the Court took place on 28 September 2009. He pleaded non-guilty to the charges brought against him.