The 550-page report by the high commissioner for human rights is the product of a "mapping exercise" that took more than two years of work, including eight months in the Democratic Republic of the Congo, the U.N. said.
Tens of thousands of people were killed, and numerous others were raped, mutilated or otherwise victimized from 1993 to 2003.
"Violence in the DRC was, in fact, accompanied by the apparent systematic use of rape and sexual assault, allegedly by all combatant forces," the report said.
High Commissioner for Human Rights Navi Pillay said a leak in August of an earlier draft that had been distributed to six countries in the region led "to intense focus on one aspect of it." That was the charge that the Rwandan army and its Congolese allies committed acts that amount to genocide.
"The report stresses that this question can only be addressed by a competent court," she said.
At least 21 armed Congolese groups and the military forces of eight other countries inside the DRC are implicated.
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