Kosovo's former president Hashim Thaci pleaded not guilty to war crimes charges in the 1990s war against Serbia as he appeared for the first time at a special international court in The Hague on Monday.

The one-time guerilla liberation hero resigned as president on Thursday and flew to the Netherlands where he was placed in the detention centre of the Kosovo Specialist Chambers tribunal.

A secial EU police unit arrested former Kosovo Liberation Army (KLA) spokesman Jakup Krasniqi at his home on the outskirts of Pristina
A secial EU police unit arrested former Kosovo Liberation Army (KLA) spokesman Jakup Krasniqi at his home on the outskirts of Pristina AFP / Armend NIMANI

Thaci, 52, is charged with war crimes and crimes against humanity including murder and torture during an alleged campaign by the ethnic Albanian Kosovo Liberation Army (KLA) against civilians it deemed to be its enemies.

"The indictment is completely without basis, and I plead not guilty to all the charges in the indictment," Thaci told the court, rising to his feet after the judge asked him if he wished to plead guilty or not guilty.

"I understood them, I heard them today, I read them, and I do not agree with any of them."

The bitter conflict killed ethnic Albanian Kosovars for the most part, and only ended when a NATO air campaign forced Serb forces to withdraw from what was then one of the country's provinces
The bitter conflict killed ethnic Albanian Kosovars for the most part, and only ended when a NATO air campaign forced Serb forces to withdraw from what was then one of the country's provinces AFP / ARMEND NIMANI

His lawyer David Hooper complained about Thaci's treatment, saying it was "disgraceful" that the ex-president was held in handcuffs outside the court, and saying he intended to seek his conditional release.

Going by the nom de guerre "Snake", Thaci was the political chief of the rebel KLA, which battled Serb forces for the independence of the southern province in a bitter conflict that claimed more than 13,000 lives.

After downing his guns following the war Thaci joined politics, leading then US vice president Joe Biden to once hail him as the "George Washington of Kosovo"

Ex president Hashim Thaci turned himself over to a Kosovo court located in The Hague where he is to face trial for war crimes and crimes against humanity
Ex president Hashim Thaci turned himself over to a Kosovo court located in The Hague where he is to face trial for war crimes and crimes against humanity AFP / Armend NIMANI

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.

Kosovo president resigns to face war crimes court
Kosovo president resigns to face war crimes court AFPTV / Kushtrim KADRIU

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.

A pedestrian walks past a mural of Russian President Vladimir Putin and US counterpart Donald Trump bearing the words "Kosovo is Serbia"
A pedestrian walks past a mural of Russian President Vladimir Putin and US counterpart Donald Trump bearing the words "Kosovo is Serbia" AFP / Andrej ISAKOVIC

The indictment accuses 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 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 Krasniqi, 69. a former Kosovar politician who was arrested by armed EU police late Wednesday in Pristina.

The other co-defendants are Thaci's closest political ally Kadri Veseli and key KLA figure Rexhep Selimi.

Many former KLA chiefs have gone on to dominate politics in Kosovo, with many still seeing him as a liberation hero, although critics see him and others as the face of a corrupt, entrenched political elite.

The charges are nevertheless a seismic moment for a young country still struggling with tense relations with Serbia, and lacking international recognition from countries like Russia since Pristina unilaterally declared independence in 2008.

Opinion on the streets was mixed.

"It's not right. The Serbs were the side that were committing crimes, killing us while they (the court) arrested those who were fighting for Kosovo," Doruntina Begu, 41, a nurse in Pristina.

The report also said there was evidence that KLA guerillas had been part of a human organ-harvesting and trafficking network operating in Albania, although an EU task force later said there was no evidence for the claims.

The fact that such "dramatic" claims were not in the current indictment cast doubt on the very legitimacy of the court, Thaci's lawyer said.

"Where are the allegations of organ theft, because they were so significant in terms of the birth of this court?" said Hooper, calling them a "most dreadful stain on Kosovo and Kosovans."