Pope Francis prayed silently alongside a senior Islamic cleric in Istanbul's Blue Mosque on Saturday, in a gesture of inter-religious harmony in a country bordering the conflicts in Syria and Iraq.

Francis took off his shoes as he entered the huge mosque, before bowing his head in prayer for several minutes, facing Mecca and standing next to Istanbul's Grand Mufti Rahmi Yaran, in what a Vatican spokesman described as a joint "moment of silent adoration" of God.

A similar act by his predecessor Pope Benedict in 2006 drew criticism from conservative Catholics and some Muslims.

Several hundred people, many of them tourists, watched from behind police barriers as the pope then walked to the nearby Aya Sofya museum, once the Christian churchHagia Sophia.

A group of school children waving Turkish and Vatican flags chanted "Long live Pope Francis" in Italian as the Muslim call to prayer rang out across the Sultanahmet square, the heart of Istanbul's historic quarter.

"We must show respect for each others beliefs. God willing the pope's visit will help in this respect," said Halil Ibrahim Cil, 24, a hospital worker from Istanbul.

"We want to practise our religion in peace. We want people to understand Islam. We don't want war."

Islamic State insurgents have captured swathes of neighboring Syria and Iraq, persecuting and killing Shi'ite Muslims, Christians and others who do not share their ultra-radical brand of Sunni Islam.

The Blue Mosque, known officially as the Sultanahmet mosque, opened in 1616 and is the most famous in Turkey. Its popular name is a reference to the fine blue Iznik tiles in its main prayer room.

Francis was later given a rapturous welcome by Istanbul's tiny Roman Catholic community when he celebrated a Mass in the city's Holy Spirit Cathedral. Several thousand people from a Catholic population of around 53,000 packed the small building and others watched from an outdoor courtyard.

He later went to a joint service with Bartholomew I, spiritual leader of some 300 million Orthodox Christians worldwide. The main purpose of his trip is to hold a joint ceremony on Sunday with Bartholomew to renew their commitment to reunite the eastern and western branches of Christianity.

Bartholomew's seat remains in Istanbul, a vestige of the Byzantine Empire, even as his flock in Turkey has dwindled to less than 3,000 among a population of 75 million Muslims.