Pope Benedict is in Turkey's largest city, Istanbul, for talks with the spiritual leader of the Orthodox churches worldwide, Ecumenical Patriarch Bartholomew.
The meeting came on the second day of a four-day papal visit to largely-Muslim Turkey.
The Vatican says the talks were aimed at healing the centuries-old divide between Roman Catholics and Orthodox Christians.
Earlier Wednesday, the pontiff celebrated Mass at a Christian shrine in southwestern Turkey, where he called for Christian unity and peace in the Holy Land and for all of humanity.
Several hundred pilgrims attended the service near the town of Ephesus, at a shrine marking the place where Christians believe Mary, the mother of Jesus, spent the last years of her life.
Pope Benedict opened his visit on Tuesday in Ankara. There, he met with Turkish leaders to promote religious reconciliation after his recent comments on Islam angered many Muslims.
He also voiced support for Turkey's entry into the European Union.
The pope triggered controversy in September, when he cited a 14th-century Christian emperor who called some of the Prophet Muhammad's teachings "evil and inhuman."
Pope Benedict has since stressed that he does not share that view, and has expressed regret for the violent Muslim backlash.
In a separate development, al-Qaida terrorists operating in Iraq denounced the papal visit, calling it part of a "crusader campaign" against Islam.
In response as reported by Associated Press, the Vatican says the denunciation shows a need for faiths to oppose "violence in the name of God."
Some information for this report was provided by AFP and AP.