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The EU harmonisation has created changes in the military's formal and informal influence in the directions of decreased formal and informal military influence in civilian politics. The EU reforms have created changes in the mindset of the citizens, by creating changes in the security culture of the citizens and in the civil-military related political culture. The desired level of alignment has not been reached. Therefore, the study examines the areas where further alignment is required. Moving from Rebecca L. Schiff's concordance theory, the article examines the relationship between the Turkish military, the civilian politics and the society before and after the EU harmonisation process. It examines the effects of the EU harmonisation process on the changes in the civil-military balance of power, and on the related security culture and political values. The analysis focuses on: (i) increased civilian control and consequent changes in the policy of accountability; (ii) transparency building in the defence sector; (iii) parliamentary oversight; and (iv) the change in the political culture related to the civil-military issues. It also investigates the extent the EU harmonisation has achieved in building democratic civil-military relations in order to align with the EU standards.