Ramush Haradinaj, a former commander of the ethnic Albanian rebels who fought against Serb forces in Kosovo's 1998-99 war, surrendered to the court on Wednesday after resigning as prime minister of the province.
In the indictment unsealed by UN judges, Haradinaj faces 17 counts of crimes against humanity for alleged murder, rape, persecution, inhumane acts, unlawful detention, deportation or forcible transfer of civilians.
Haradinaj also faces 20 counts of violations of the laws or customs of war for cruel treatment, murder and rape.
As the commander of the Kosovo Liberation Army, Haradinaj "personally ordered, controlled and participated in beatings" of civilians, the indictment said.
Haradinaj, 36, could face life imprisonment if convicted of any of the charges. He is expected to appear in court in coming days, when he will be asked to enter a plea.
Lahi Brahimaj, another suspect named in the indictment, travelled to the court with Haradinaj.
Brahimaj was a former rebel and a member of the Kosovo Protection Corps, a civilian emergency group made up of ethnic Albanian former rebels.
A third former rebel, Idriz Balaj, also was indicted by the court and surrendered on Wednesday.
International officials praised Haradinaj - a seasoned battlefield commander with a fiery temper and a loyal following - for his decision to surrender to the court and called on other countries in the region to follow his example.
'Haradinaj personally ordered, controlled and participated in beatings' of civilians'
UN tribunal indictment
UN prosecutors accuse him of responsibility for crimes committed by subordinates and of personal involvement in atrocities.
The indictment said that Haradinaj's forces drove Serb and Roma civilians from villages "and killed those civilians that remained behind".
Balaj, serving under Haradinaj, ran a special unit known as the Black Eagles which "repeatedly abducted, beat, mutilated, tortured and murdered civilians and detained persons taking no active part in hostilities", the indictment said.
It charged that he raped a Roma woman and tortured a prisoner at a detention centre, and attempted to cover up civilian murders by having victims' bodies thrown into a lake.
In the second half of May 1998, "a makeshift detention centre was established at the KLA headquarters in Jablanica where at least 16 noncombatants were detained, beaten and tortured", it said.
"One is known to have died while the others are still missing", the indictment said.