Istanbul is also important as being the center of one of the biggest debates in the Christian world since the 6th century as The Greek Orthodox Patriarchate is located in Fener (Phanar) neighbourhood of Fatih district.

After the conquest of Constantinople by Turks, Sultan Mehmed The Conqueror granted legal protection to the Greek Orthodox Partriachate in Istanbul.

The Patriachate was originally located in The Havariun Church, in today's Fatih district. The church was built on grounds of the Constantinus's mausoleum. (Some sources say that the Church was orderd to be built by Constantinus himself.) Later on the Patriachate was moved to Pammakaristos Monastery (Today's Fethiye Mosque) due to decreasing number of the christian population and security reasons in 1455.  (Later on Sultan Mehmet built the Fatih Mosque on the Havariun Church's site.)

Pammakaristos Church was relatively smaller than the The Havariun Church, and it was restored and expanded in 1518. After, the Patriarchate moved to Vlah Palace Church in Fener, then to Ayios Dimitrios Church in Ayvansaray districts. Finally it was moved to Ayios Yeoryios Monastery in Phanar district in 1602.

The Patriache, was considered a Vezier in the Ottoman government and also attended Divan meetings at the palace. Also was exempt from taxes, had legal decision rights for the issues among the orthodox people of the empire, and perhaps had more power over the Orthodox citizens of the empire than ever before during the Ottoman period.