Thaci led the fight against Serbian forces in 1998-1999 as a commander in the Kosovo Liberation Army and oversaw the country's declaration of independence 12 years ago.
Kosovo's first prime minister, he has been president since 2016, but stepped down to face allegations at the Kosovo Specialist Chambers of responsibility for detaining, torturing and killing wartime opponents to gain political control of the contested region.
Thaci is being held in the same detention center in the Dutch coastal town of Scheveningen where his main rival, Serbian President Slobodan Milosevic, died in custody in 2006 during his trial for alleged Balkan war crimes.
Thaci is expected on Monday to challenge the legitimacy of the EU-backed court, which in recent weeks has arrested six other leading former KLA commanders.
Prosecutors say Thaci, 52, was responsible for nearly 100 murders of civilians. He could face a maximum sentence of life imprisonment if convicted by the tribunal, which has international judges and prosecutors but applies Kosovo law.
Thaci has previously denied all the allegations.
During a hearing starting at 3 p.m. (1400 GMT), Thaci will have the charges explained by a judge. He has 30 days to enter a plea.
After initially helping set up the court under pressure from the international community, Thaci has since tried on three occasions to revise the Kosovo constitution to block it.
In Kosovo, many see the KLA commanders as heroes who freed the country from Serbia's repressive regime against Kosovo's ethnic Albanians.The Kosovo tribunal was set up in 2015 to handle cases relating to alleged crimes by KLA members during and after the 1998-99 conflict, which led to Kosovo's independence from Serbia a decade later in 2008.