This dissertation analyses the impact of the dynamics of Turkey and Greece's institutional links with the European Union and NATO on the nature of Turkish-Greek relations from an International Relations theoretical perspective. In undertaking this task the main research interest is to uncover the impact of links with international institutions on the security identities of states. Relevant theoretical approaches, namely rationalist institutionalist theories of neo-liberalism and neo-realism and sociological institutionalist theory of social constructivism, are assessed in terms of their capabilities to explain the relationship between links with international institutions and security identities of states. In this regard, this dissertation mainly draws on the social constructivist approach for the main reason that the rationalist institutionalist theories fall short of offering convincing explanations as to the identity transforming effects of interactions within institutional environments. The main argument is that the contextual environment of Turkey and Greece’s interaction through the EU and NATO has contributed to the perpetuation of realpolitik security identities and practices in and around the Aegean Sea and Cyprus, rather than setting the stage for long-term cooperative bilateral relations based on non-realpolitik security identities. In this sense, the realpolitik kind bilateral security relations are ideational in nature and have been to a significant degree informed by the context of Turkey and Greece's joint membership in NATO and close relations on the margins of the European Union. This dissertation simply tries to unravel the mechanisms through which this outcome has taken place. Assuming that Turkey and Greece would have stable and long-term cooperative security relations if and only if their security identities and interests came closer to each other on the basis of the non-realpolitik security norms of the western international/security community, this dissertation argues that the way the dynamics of Turkey and Greece's institutional relations within the EU and NATO frameworks have unfolded has significantly curtailed this possibility. By way of conclusion, this dissertation has reached the following points: First, the social constructivist approaches are better equipped with the tools to highlight the identity-transforming effects of links with international institutions. Second, the alleged security community identities of the European Union and NATO have not contributed to the emergence of a security community between Greece and Turkey. This was so because NATO has been a collective defence organization of realpolitik kind since its inception. Besides, the European Union members have acted towards Turkey and Greece from an instrumental perspective, highlighting the costs and benefits of their true inclusion in the Union, rather than from the logic of appropriateness believing that their incorporation into the Union would be in accordance with the security identity of the Union. Third, for Turkey and Greece to develop a non-realpolitik security relationship within the framework of the European Union they should approach the EU from an ideational perspective, rather than an instrumental one. They should believe that the resolution of their territorial disputes in peaceful ways would be legitimate in order for them to be considered as real Europeans.