Twenty-five years after the fall of communism, the Balkans is facing numerous security threats. Particularly, militant Islamism becomes a serious threat to the fragile stability in the region. The expansion of militant Islamist organizations that are able to join global cooperation over the fulfillment of ideological goals is a serious threat to national and regional security. Even though the activities of these organizations do not differ much from those from the other parts of the world, yet Bosnia and Herzegovina, Albania, and Kosovo deserve special attention. Some of their political and religious leaders have had long and strong relations with the Muslim Brotherhood and Al Qaeda. Also, the militant Islamists have established a solid ground for re-islamization of the Muslim population, their radicalization, and recruiting for the jihadist’s frontlines. In this paper, the factors that influence the expansion of militant Islamism and the specific methods of acting in the countries of the Western Balkan are researched