Making his initial appearance since being transferred from the Democratic Republic of Congo (DRC) on 21 September before presiding judge Rashida Khan, Ndahimana responded ‘'Not Guilty'' to all four counts read out to him.
He is charged for genocide or alternatively complicity in genocide, conspiracy to commit genocide and extermination as crimes against humanity.
The Judge has ordered the Registry to fix a date for the trial's hearing.
Ndahimana was arrested in North Kivu, eastern DRC.
The accused is in the list of 13 fugitives for whom the United States government has offered a bounty of $five million for any information leading to their arrests.
Ndahimana is alleged to have helped to organize the genocide and also supervised the killings of ethnic Tutsis in his commune.
According to the ICTR indictment, he is responsible for the deaths of at least 2,000 Tutsis, most of whom were killed when Hutus bulldozed a church in Kibuye, western Rwanda, where they had sought refuge.
‘'After the destruction of the Church, most of the Tutsis from Kivumu commune were killed, and in July 1994, there was no Tutsi known in the commune,'' claims the prosecution.
Most of the former Rwandan military and Interahamwe militia members responsible for the genocide fled to Rwanda's giant western neighbour, Congo, after Tutsi rebels, the Rwanda Patriotic Front (RPF), came to power in July 1994 and ended the bloody massacres.
The UN Court since its establishment in November 1994 by the UN Security Council has so far convicted 36 persons and acquitted six.
© Hirondelle News Agency