The Holy See has a history of difficult relations with Turkey, or rather with the Ottoman Empire, whose forces its European allies defeated at the naval battle of Lepanto in 1571 and the battle of Vienna in 1683. The Holy See maintained positive relations with Armenia, even when it was under Ottoman rule. It was also involved in the Balkans and Greece at a time when nationalities were emancipating themselves from Turkish domination.
The Atatürk revolution did not really ease relations, since it led to the suppression of the millet system, which had previously guaranteed the rights of Christian minorities that were split in Byzantine, Latin, Armenian, Syriac and Greek-Melkite ethnic lines. This is in turn led to the assimilation of Turkey's Christian population into ethnic Turkish traditions and customs. Also, the Kemalist ideology was closely related to anticlericalism in France, a French republican ideology which had been hostile to the Church in Western Europe.
The Holy See has maintained positive relations with the Ecumenical Patriarch of Constantinople since the 1960s. The Ecumenical Patriarch who is based in current day İstanbul is not recognized as leader of the Eastern Orthodox by the Turkish government, which prefers to regard him as a local bishop. This non-recognition of the Patriarch is an issue in Holy See–Turkey relations. The Church has also sought to have improved legal recognition of itself under Turkish law, which at present makes it difficult for Catholic bishops to be legally recognized in their exercise of Apostolic ministry, while at times the ownership of churches is put into question. Similar problems have come up with the Greek Patriarchate, whose seminary training was shut down by the Turkish state.
Armenian genocide
In 2000, John Paul II officially recognized the Armenian Genocide, an opposing position to that of the Turkish government which has deployed much of its political energies in having the events in Armenia remain unrecognized by the international community. On 12 April 2015, Pope Francis used the term 'genocide' to refer to mass killings of Armenians by Turks. In response, Turkey recalled its ambassador to the Vatican for "consultations" just hours after Francis' comments, and summoned the ambassador from the Vatican for a meeting. Also, on June 24, 2016, Pope Francis in another speech described the killing of Armenians as a genocide. In addition, the Vatican spokesman Federico Lombardi, told the reporters that "There is no reason not to use this word in this case," "The reality is clear and we never denied what the reality is." Turkey condemned the declaration as “very unfortunate” and also said that it bore traces of “the mentality of the Crusades.”
Relations exist between the Holy See and Turkey on the basis of tourism and pilgrimages. In the 2008-2009 Year of Saint-Paul, an agreement was reached between the two States in order to promote pilgrimages to Tarsus, the place that the apostlePaul was born. Other important pilgrimage sites include Selçuk, the old city of İstanbul, İznik, Bergama, İzmir, Manisa and Trabzon.