Both leaders have called for restored Christian unity between the two churches.
The meeting was the first between a Pope and a Russian Church head since the Western and Eastern branches of Christianity split in the 11th Century.
In a joint declaration, Pope Francis and Patriarch Kirill also urged the world to protect Christians from persecution in the Middle East.
The two-hour talks took place during Pope Francis’s stopover on his way to Mexico. Patriarch Kirill is visiting Cuba, Brazil and Paraguay.
The two leaders embraced and kissed each other at the start of the meeting on February 12.
“I’m happy to greet you, dear brother,” the Russian Church leader said.
“Finally,” Pope Francis said.
At a news conference after the meeting, Patriarch Kirill said the discussions were “open” and “brotherly”, while Pope Francis described them as “very sincere”.
“We hope our meeting contributes to the re-establishment of this unity wished for by God,” their joint declaration said.
The document called on the world community to defend Christians, saying that “in many countries of the Middle East and North Africa whole families, villages and cities of our brothers and sisters in Christ are being completely exterminated.”
“Their churches are being barbarously ravaged and looted, their sacred objects profaned, their monuments destroyed.”
Patriarch Kirill has been the head of the Russian Orthodox Church since February 2009, while Pope Francis took up his role in March 2013.
The Roman Catholic Church has more than a billion members worldwide, while the Russian Orthodox Church numbers about 165 million.
The Russian Church is the largest and most powerful in the Orthodox faith, which is made up of a number of separate churches.
Vatican has ties with Istanbul-based Ecumenical Patriarch of Constantinople Bartholomew I – nominal head of Eastern Orthodox Churches, but Cuba talks is the first between a Pope and a Patriarch of Russian Church.
The Russian Church is the largest and most powerful Church in Orthodoxy.
Cuba was reportedly chosen as the place of their first meeting because it is far from Rome, Istanbul and Moscow with all their historical baggage of schism.
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