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The Ad Hoc Tribunal acquitted the Accused of both charges, as it found none of his subordinates to have committed serious human rights abuses. In addition, the Tribunal found that the Accused has not disregarded important information and has acted in the best of his power to stop the human rights violations.

East Timor’s foreign minister described the judgment as ‘scandalous’, whereas activists in Indonesia considered the judgments of the Ad Hoc Tribunal to be “mock trials...[as] a result of pressure from the military.” Florendo de Jesus, one of the witnesses, testified that he had recognized several people among the attackers as TNI (Indonesian National Armed Forces) members, one of them being his own uncle. The public outrage, mostly taking place in East Timor, came as a consequence of a belief that the Ad Hoc Tribunal is failing to try the Indonesian commanders involved in the violence, as well as from the previous acquittals, specifically those of army Lieutenant Colonel Asep Kuswani, police Lieutenant Colonel Adios Salova and mayor Leonita Martins.

The Ad Hoc Tribunal acquitted the three defendants of the charges entered against them and found that the prosecution had not been able to establish a link between the TNI (Indonesian National Armed Forces) and Polri (Resort Police of the Police of Republic of Indonesia), on the one hand, and the BMP, on the other. The former were official governmental bodies, whereas the latter were militia. The judgment was publicly criticized as it was argued that the TNI and the riot police were indeed involved in the violence, including the killing of the 22 civilians.

On 21 February 2003, Trial Chamber I of the ICTR delivered its unanimous judgment on the case of Elizaphan and Gérard Ntakirutimana. Gérard Ntakirutimana, a medical doctor practicing at the Mugonero Adventist hospital, was convicted of genocide and of crimes against humanity (murder). His father, Elizaphan Ntakirutimana, a senior pastor of the Seventh-day Adventist church in Mugonero was convicted of aiding and abetting in genocide.

The two Accused jointly faced two indictments, the “Mugonero” indictment with five counts and the “Bisesero” indictment with seven counts. Both indictments charged them with genocide, in the alternative complicity in genocide, conspiracy to commit genocide as well as crimes against humanity. The Accused allegedly participated in killings, attacks and caused serious bodily and mental harm to a large number of men, women and children who sought refuge in the Mugonero Adventist complex as well as in the area of Bisesero.

Pastor Ntakirutimana was sentenced to ten years of imprisonment while his son, Gérard, was sentenced to imprisonment for twenty five years. In both cases credit was given for the time they had already served in the United States and in Arusha.

On 1 December 2003, Trial Chamber II of the ICTR sentenced Kajelijeli to two concurrent life terms for genocide and extermination as a crime against humanity and to an additional 15 years imprisonment for direct and public incitement to commit genocide. All three sentences were to run concurrently.

The Appeals Chamber overthrew Kajelijeli's cumulative convictions for genocide and extermination as a crime against humanity under Counts 2 and 6 insofar as they were based upon a finding of command responsibility. However, the Appeals Chamber found that the Trial Chamber was required to take its finding on Kajelijeli’s superior position (Article 6(3)) into account at sentencing as an aggravating factor. The Appeals Chamber found that the Trial Chamber had done so. The appeal was dismissed in all other respects.

However, the Appeals Chamber ruled that in view of the serious violations of his fundamental rights during his arrest and detention in Benin and at the UN detention facility from 5 June 1998 to 6 April 1999, the two life sentences and the 15 year sentences which were to run concurrently imposed by the Trial Chamber should be converted into a single sentence of imprisonment for 45 years. The Appeals Chamber ordered that Kajelijeli be given credit for time already served in detention.

Léon Mugesera, a former politician of the party the National Republican Movement for Democracy and Development (MRND) in Rwanda, fled Rwanda in 1993 – before the actual start of the Rwandan genocide in 1994 – after the authorities had issued an arrest warrant against him for incitement to genocide and murder, as he had given one of the first inflammatory public speeches that eventually led to the genocide. Mugesera, together with his wife and their five children, sought asylum in Canada, which was granted. However, in 1995, the Immigration and Refugee Board became aware of the arrest warrant and issued an order to deport Mugesera to Rwanda for trial.

After several years of litigation, the Federal Court of Appeal held that the deportation order should not have been issued as there was not sufficient evidence that Mugesera had indeed been involved in the Rwandan genocide as alleged. However, the Canadian Supreme Court quashed this decision on 28 June 2005, ruling that the Court of Appeal had applied an incorrect standard of review and that, in fact, the Immigration and Refugee Board had been right all along. The deportation order was affirmed.