Mr Thaci has repeatedly proclaimed his innocence and claims the international system of justice is “rewriting history” over the conflict. On Thursday he said he was stepping down as president to “protect the integrity” of the office.
The bitter conflict killed ethnic Albanian Kosovars for the most part, and only ended when a NATO air campaign forced Serb forces to withdraw.
Top Serbian military and police officials were later convicted of war crimes in other international courts.
But rebel leaders of the KLA have also been accused of revenge attacks on Serbs, Roma and ethnic Albanian rivals during and after the war.
The indictment accuses Mr Thaci and three others of war crimes and crimes against humanity, including murder, torture, illegal detention, enforced disappearances and persecution, committed between 1998 and 1999.
They allegedly carried out “a widespread or systematic attack against the civilian population”, including those believed to be collaborating with Serb forces, or not cooperating with the KLA.
Former KLA spokesman Jakup Krasniqi, one of Mr Thaci’s co-defendants, pleaded not guilty to the charges when he made his first appearance at the court on Monday.
“It is not right that I am here, an injustice has been done against me,” said Mr Krasniqi, 69. a former Kosovar politician who was arrested by armed EU police late Wednesday in Pristina.
The other co-defendants are Mr Thaci’s closest political ally Kadri Veseli and key KLA figure Rexhep Selimi.