A former regional commander of the Kosovo Liberation Army (KLA), Haradinaj is accused of leading attacks against ethnic Albanian and Roma civilians.
He is also said to have masterminded a campaign to drive Serbs and Roma from their villages.
Kosovo Liberation Army
KLA forces, including a special unit called the "Black Eagles", killed those civilians left behind or those who refused to abandon their homes, according to the indictment.
Idriz Balaj, the commander of the "Black Eagles", and Lahi Brahimaj, Haradinaj's uncle who worked closely with the former prime minister within the KLA, will also stand trial.
They also pleaded not guilty on Thursday to the amended war crimes charges.
The Kosovo Liberation Army fought for independence from Serbia and Montenegro

A former nightclub bouncer in Switzerland, Haradinaj was appointed prime minister in late 2004.
He resigned in 2005 and surrendered to the UN to face charges of murder, rape and torture allegedly committed by forces under his command.
Haradinaj is the most senior former KLA leader to be indicted over the war against Serb forces and the first serving head of government to be indicted since Slobodan Milosevic, the former president of then-Yugoslavia.
He is held in great respect by many Kosovo Albanians, last week urging them not to destroy Kosovo's possible independence from Serbia through impatience.
Kosovo violence continues
Kosovo has been administered by the UN since a Nato bombing campaign drove Serb forces out of the province, populated mainly by ethnic Albanians, in 1999.
Two people were killed in clashes between police and ethnic Albanians in Kosovo this month and the bombing last week of three parked UN vehicles underscored fears of unrest after the UN recently unveiled plans for Kosovo's eventual independence.
Analysts say Haradinaj remains the most influential figure behind the coalition government and credit him with keeping Albanian tempers in check. The trial is due to begin on Monday.