A special prosecutor in The Hague announced preliminary indictments against Thaci in June, just days before he was to attend a White House meeting with Serbian President Aleksandar Vucic intended to achieve a breakthrough between their countries. President Trump has made normalizing relations between the two countries a foreign policy priority.
The allegations date to his time as a commander in the Kosovo Liberation Army in incidents between March 1998 and September 1999. As a senior leader in the guerrilla force, Thaci knew of killings, torture and other persecution of civilians believed to be opponents and did not act to stop the crimes, according to the indictment.
The court said Thursday that Thaci and other top Kosovo Liberation Army officials were responsible for a “widespread and systematic attack against persons suspected of being opposed to the KLA.”
Thaci told reporters in Pristina, the Kosovo capital that he was stepping down “to protect the integrity of the presidency of Kosovo” before flying to the Netherlands. He has denied the charges. Vjosa Osmani, the head of Kosovo’s parliament, has taken over as acting president pending the election of a new leader.
Thaci had been president since 2016. He has been a dominant figure in Kosovo’s political life for decades, evolving from separatist militia leader into a politician once the territory achieved autonomy from Serbia. He was prime minister of Kosovo when it declared independence in 2008.
Other top Kosovo Liberation Army officials, many of them active in Kosovo political life, also face charges. Kadri Veseli, Thaci’s successor as the leader of the Democratic Party of Kosovo, also resigned his position Thursday and voluntarily went into custody in The Hague.
“I see it as an opportunity to finally respond to these false suspicions and rumors which have been circulating for years,” Veseli said in a statement.
On Wednesday, Jakup Krasniqi, another former Kosovo Liberation Army leader, was arrested in Pristina and transferred to The Hague. Krasniqi is a former speaker of parliament.
The special Chamber in The Hague is staffed with international judges and prosecutors but operates under Kosovo law.
The 1998-1999 war in Kosovo between Yugoslav forces and the Kosovo Liberation Army ended after a 78-day NATO air campaign. It led, nine years later, to Kosovo’s declaration of independence. Serbia never recognized Kosovo’s statehood, and the unresolved borders have prevented full stability in the Balkans ever since. European officials have said the conflict must be resolved before Serbia can join the European Union.
The European Commission “welcomes” Thaci’s decision to submit to the court proceedings, Peter Stano, a spokesman for E.U. foreign policy chief Josep Borrell, said in a statement. “Full cooperation with these institutions is essential as an important demonstration of Kosovo’s commitment to the rule of law.”
Thaci has been negotiating for years with Vucic, who was on the other side of the Kosovo war as a minister in the Federal Republic of Yugoslavia, to normalize relations between Pristina and Belgrade. But the two sides have not been able to agree on what to do about pockets of ethnic Serbs in Kosovo and Albanian-speaking communities within Serbia.
Trump deputized Richard Grenell, a former ambassador to Germany and acting national intelligence director, as an envoy to try to resolve the conflict.
Trump ultimately met in September with Vucic and Kosovo Prime Minister Avdullah Hoti in the White House, where the two sides announced an agreement to bolster their economic ties. But a full, final mutual recognition has remained out of reach.