In the aftermath of the Cold War, the traditional concept of defense and security no longer represents an adequate response to the new security challenges and threats that the international community faces. Since the war in Bosnia in 1991, the Euro-Atlantic community became aware of the necessity to reform its security sector so as to tackle such problems as global terrorism, organized crime, intra-state ethnic and religious conflicts, as well as the abuse of human rights. The growing demand for respect of democracy and human rights suggest that this reform should not focus solely on strict security institutions, but it should also include political and civilian institutions. The SSR agenda provides for a holistic and concrete response to all security related problems, but, as past experience demonstrates, many difficulties arise in the implementation stage; attempts to operationalise SSR proved to be problematic in certain contexts as are the post-Communist Central and Eastern European countries. This paper describes specific problems that arose during the implementation stage of the SSR agenda in Bosnia and Herzegovina, Croatia, Bulgaria, Russia, Kosovo, and Serbia, and suggests different recommendation policies in order to successfully engage in a holistic, cohesive, and strategic amelioration of the security sector.