NATO’s supremacy in the security and defence structures of the Euro-Atlantic region during the Cold War era has prevented the development of a self-sustained European security mecha- nism. With the end of the Cold War, specifically with the St. Malo Summit in 1998 which was a breakthrough in the advancement of the Common Security and Defence Policy, the NATO-EU relationship became pronounced. Since then, opportunities for and difficulties of collaboration have both defined this inter-institutional relationship between NATO and the EU. Despite a series of arrangements for strengthening the institutional framework of NA- TO-EU relations as well as the Berlin-plus agreements, the argument of an effective coopera- tion between two organizations would be misguided. Particularly, discrimination against the non-EU NATO allies as well as the existence of challenges such as decoupling and duplication are hampering progress in NATO-EU relations. This article aims at shedding a light on the limited cooperation between these two organizations by focusing on the current challenges.