The internecine warfare in the former Yugoslavia has radicalised many Islamic movements in the region and facilitated close links between local Balkan groups and Middle East states as well as terrorist organisations. This article examines the spread of militant Islamic fundamentalism in the Balkans as well as in Kosovo, Macedonia, Bulgaria, Turkey, and Albania. The scope of linkages between Balkan Islamic movements and Iran pose serious concern for Western governments as a long‐term threat to any stability and democratisation in the Balkan region as it has intensified illegal activity throughout the area and heightened irredentist claims.