Obed Ruzindana was arrested, at the request of the Chief Prosecutor of the ICTR (International Criminal Tribunal for Rwanda), on 20 September 1996 in Nairobi, Kenya. On 22 September 1996, he was transferred to the prison quarters of the United Nations in Arusha, Tanzania
At his initial court appearance, on 29 October 1996, Ruzindana pleaded not guilty to all of the 6 counts with which he was charged. The ICTR ordered that the trial of Obed Ruzindana be combined with that of Clement Kayishema (see "related cases"). Their trial was opened on 11 April 1997. After hearing a number of witnesses, the Chamber retired to consider its verdict on 17 November 1998.
On 21 May 1999, the Second Trial Chamber of the ICTR pronounced its verdict and declared-unanimously – Obed Ruzindana to be guilty of “genocide” (19th count of the indictment – for the massacre committed in the Bisesero region). Ruzindana was found not guilty of war crimes and other inhumane acts as a crime against humanity.
Moreover, the Chamber declared-by a majority verdict- that Ruzindana was not guilty of “extermination as a crime against humanity” and not guilty of “murder as a crime against humanity” since, it was the considered opinion of the Chamber, that these two counts were wholly included in that of genocide. Judge Tafazzal Hossain Khan, however, issued a dissenting opinion in this respect.
Ruzindana was sentenced to 25 years imprisonment by the ICTR.
He appealed his conviction, but on 1t June 2001, the Appeal chamber of the ICTR confirmed the verdict of the Trial Chamber.
On 9 December 2001, he was transferred to Mali to serve out his sentence.