The traditional model of harmony and interfaith tolerance that had existed in Kosovo and the countries of the region for centuries has come more and more under attack in recent times. Unfortunately, recently, the traditional model of religious harmony and tolerance that has been cultivated for centuries in Kosovo has begun to be attacked. After the war in Kosovo, started the uncontrolled arrival of some “humanitarian” organizations in the region and the departure of dozens of Kosovar youths for religious education began in some Islamic Middle East centers. Some people and asociation from the Near East, came as “missionaries” began their subversive activity in promoting Islamist extremism and spreading a radical ideology in all inhabited areas with Muslim populations in the Balkans. The risks of terrorist attacks by Islamist extremists in Kosovo and the countries of the EU still seem to be limited. However, if the political and social crisis escalates in Kosovo and the conflict in the Middle East is exacerbated, which could also lead to a polarization of the public’s attitudes toward Islam, the danger of terrorist attacks by Islamist extremist can’t be ruled out any more in both to Kosovo and the EU countries.