In the post Cold War era, the dimension of the threat and means of attack changed when compared with the Cold War era. The threat became unpredictable, unforeseeable and unclear. In the new geo-politic era, new threats such as terrorism, weapons of mass destruction, extremism or organized crime cause growing instabilities in the regions. Although significant progress has been obtained in terms of stability in the Balkans, it is still among areas of interest and should be analyzed within this regard, as some risks have the potential to become threats if neglected. The Balkans, which keeps its strategic status between the Middle East and Western Europe, faces organized crime, ethnic rivalries and extremism in different levels. Widespread unemployment, immature economy and governance challenges are the main factors having effects on the aforementioned sources of instability. In the changing dimension of asymmetric threats and asymmetric warfare, today's challenges require more awareness than before as they are becoming more complex.