The mainstream Hanafite school of Sunni Islam is largely organised by the state, through the Diyanet Isleri Baskanligi (Religious Affairs Directorate), which controls all mosques and Muslim clerics. The directorate is criticized by some Alevi Muslims for not supporting their beliefs and instead favoring the Sunni faith.

The Ecumenical Patriarch of Constantinople (Patrik) is the head of the Greek Orthodox Church in Turkey, and also serves as the spiritual leader of all Orthodox churches throughout the world. The Armenian Patriarch is the head of the Armenian Church in Turkey, while the Jewish community is led by the Hahambasi, Turkey'sChief Rabbi, based in Istanbul. All these groups share the same criticism of the directorate.