Francis and Ecumenical Patriarch Bartholomew I issued a joint declaration urging leaders in the region to intensify help to victims of the Islamic State group, and especially to allow Christians who have had a presence in the region for 2,000 years to remain on their native lands.
"The terrible situation of Christians and all those who are suffering in the Middle East calls not only for our constant prayer but also for an appropriate response on the part of the international community," they wrote.
He was also set to meet with a few of the 1.6 million refugees who have crossed into Turkey to flee the IS assault in neighbouring Syria and Iraq.
Francis, who represents the 1.2 billion-strong Catholic Church, and Bartholomew, the spiritual leader of the world's 300 million Orthodox Christians, called for "constructive dialogue" with Islam "based on mutual respect and friendship."
"Inspired by common values and strengthened by genuine fraternal sentiments, Muslims and Christians are called to work together for the sake of justice, peace and respect for the dignity and rights of every person, especially in those regions where they once lived for centuries in peaceful coexistence and now tragically suffer together the horrors of war," they said.
The Vatican had downplayed the meeting, perhaps because of organisational glitches or to not distract from Francis' ecumenical activities which were the main reason for the visit.
But just before the trip began, the Vatican revealed that he would indeed deliver a speech to the youths.
Francis kicked off his final day in Turkey with a liturgy alongside Bartholomew in the Orthodox Church of St George, where incense mingled with hypnotic chants on an important feast day for the Orthodox Church.
At the end of a joint prayer service yesterday evening, Francis bowed to Bartholomew and asked for his blessing "for me and the Church of Rome," a remarkable display of papal deference to an Orthodox patriarch that underscored Francis' hope to end the schism.
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