The Pope continued his visit to Turkey Saturday by meeting local leaders of the Armenian, Syrian, Chaldean and Latin Catholic churches.
They form small Christian minorities in an overwhelmingly Sunni Muslim Turkey. Less than one percent of Turkey's 76 million inhabitants are Catholic.
In the afternoon, he celebrated mass in the Cathedral of the Holy Spirit, before a congregation that included Protestants and the spiritual leader of the world's Orthodox community, Ecumenical Patriarch of Constantinople Bartholomew.
The Orthodox leader obliged, kissing Francis' bowed head. The two major branches of Christianity represented by Bartholomew and Francis split in 1054 over differences on the primacy of the papacy, giving particular resonance to Francis' display of deference.
In his sermon, Francis appealed to Christians in Turkey and the world over to unite in the face of discord, calling the diversity of the Christian faith a "tremendous potentiality."
A prayer in the Blue Mosque
That message came after the Pope had visited one of Turkey's most important religious sites, the Blue Mosque, together with Istanbul's Grand Mufti Rahmi Yaran.
Francis removed his shoes as he entered the Sultan Ahmet mosque, widely known as the Blue Mosque, and was taken through by Yaran.
The two paused for two minutes facing Mecca alongside each other, the pope closing his eyes, bowing his head and clasping his hands as he performed a Muslim prayer.
"We are in need of prayers. The world really needs prayers," Yaran said afterwards.
Vatican spokesman Reverend Federico Lombardi described the act as a "moment of silent adoration" before God.
A similar act by Pope Francis' predecessor, Pope Benedict XVI, in 2006 drew widespread criticism following a speech in which Benedict linked Islam with violence.
The pope then toured the Hagia Sophia, formerly the main Byzantine church in what was once Constantinople, before it was turned into a mosque after the Ottoman Turks conquered the city in 1453.
Since 1935, the building has been a secular museum.
The Pope visit to Turkey has drawn strong media attention, given that Turkey borders Iraq and Syria where the self-declaredIslamic State militant group is waging a campaign of persecution against those who do not follow its radical doctrine.
Saturday's visits were conducted amid heavy security, though Pope Francis kept with his custom of traveling in a modest vehicle.
The three-day visit is seen as a test of Francis' ability to build bridges between faiths, as well as establish and strengthen ties with Muslim leaders while condemning attacks on Christians and other religious minorities underway in the Middle East.
The visit is set to culminate on Sunday with a joint celebration of the Feast of St Andrew, the patron saint of the Orthodox world, alongside Bartholomew.
glb/ipj (Reuters, AFP, AP, dpa)