The EU accession process reveals a series of paradoxes, which are not merely indicative of the complexity of Turkey's state-religion relations in general but also point to how the Justice and Development Party (JDP) government portrays controversies such as the Sunni-Alevi divide. The religious cleavages in Turkey have become Europeanized and found expression in the European political and legal structures. The Alevis have been one of the groups most affected by this issue partly because of their heterodox and transnational religious identity and partly as a result of their links with secularist political sectors. The paper underlines a dilemma of current Turkish politics. The case of the Alevis shows that the regime's current transformation undermines its basis through exclusion. The JDP's political strategy, focusing on the effective control of the mainstream Sunni base, does not willingly accept or tolerate the autonomy of some civil society groups, including the Alevis.