Çeku had developed contacts with the KLA in the mid-1990s. When war broke out in Kosovo, the KLA initially did very badly against the Yugoslav forces, due in part to poor leadership under senior commander Sylejman Selimi, a militarily inexperienced individual who had been given the post largely because of his influence in the Drenica region. In May 1999, Çeku was appointed the KLA's chief of staff, replacing Selimi. He immediately set about reorganising the KLA and implementing a proper military structure within the organization. In the closing days of the Kosovo War, the KLA began providing systematic intelligence to NATO as well as mounting attacks to lure Serbian forces into the open, enabling NATO warplanes to bomb them. According to reports at the time, Çeku was the principal liaison between NATO and the KLA.
Kosovo Protection Corps
Following the end of the war in June 1999, Çeku oversaw the demilitarisation of the KLA and its transformation into the Kosovo Protection Corps, an ostensibly civilian organization charged with disaster response, demining, search and response and humanitarian projects. Although the international community insisted the KPC was a civilian organization, Çeku and its membership said they believed the KPC should evolve into the future army of an independent Kosovo. Çeku managed ably many difficult challenges for the KPC, including allegations that its members were supporting the ethnic Albanian insurgency in Macedonia in 2001.
Political career
On 10 March 2006, Çeku was elected Prime Minister of Kosovo by the Kosovo Assembly. After being sworn in, he declared his support for Kosovo independence, whilst promising to protect the rights of the Serbian minority. Çeku's appointment was backed by former Prime Minister Ramush Haradinaj, who resigned in early 2005 after the ICTY had indicted him for war crimes. In his first one hundred days in office, Çeku prioritized the implementation of the UN-endorsed "Standards" for good governance and multi-ethnicity, earning praise from UN Kosovo chief Søren Jessen-Petersen and Contact Group countries. On 24 July 2006, Çeku traveled to Vienna for the first high-level meeting between the Presidents and Prime Ministers of Serbia and Kosovo to discuss Kosovo's future status. He stated that he would found a new political party after stepping down as PM, dispelling rumours that he would join the Reformist Party ORA. However, he joined the Social Democratic Party of Kosovo on 10 April 2008, and did not rule out that the party would unify with ORA. On 23 February 2011, Çeku was made Minister of Security Forces of Kosovo.
The Serbian government has accused Çeku of war crimes. Although Çeku has not been the subject of any ICTY indictment, he was briefly detained in Slovenia in October 2003 and in Hungary in March 2004 on the basis of an Interpol warrant issued by Serbia. Çeku was quickly released in both instances following pressure by the UNMIK. The ICTY issued the last indictments in late 2004 and limited all further investigations to ongoing cases only. In May 2009, Colombian authorities expelled Çeku from a conference held in the country due to Serbia's extradition request based on possible war crimes committed by him during the Kosovo War. On 23 June 2009 he was arrested in Bulgaria under the Interpol arrest warrant issued by Serbia for alleged war crimes in Kosovo against non-Albanian population. The Bulgarian authorities decided to release him from custody, but requested that he remain in the country for up to 40 days as officials consider Serbia's extradition request. On 30 June, he returned to Kosovo, after the Bulgarian prosecutors decided not to appeal the court's decision for his release.
Family life
He is married to Dragica, who is half-Serbian, half-Croatian. They have three children and the family divides its time between Pristina and the Croatian town of Zadar.