Pope Francis and the Russian Orthodox Patriarch Kirill have embraced at what is the first meeting between the leaders of the two branches of Christianity since a schism nearly a thousand years ago.

The historic meeting took place at an airport terminal in Cuba, where the two issued a message of unity.

The Pope was on a long-scheduled trip to Mexico, but added the stop in Cuba in order to meet the Patriarch.

"Finally," Francis said as he and Kirill entered through doors on opposite sides of a room at Havana airport. "We are brothers."

The two joined arms and kissed on both cheeks, Francis dressed in white with a skullcap, and Kirill wearing a tall, domed hat that dangled a white stole over black robes.

Cuban President Raul Castro was also present at the ceremony, but let the two religious leaders take the limelight.

Eastern Orthodoxy split with Rome in 1054 and the leaders of the Eastern and Western branches of Christianity have not met until now.

But early on in his papacy, Francis issued a standing invitation to meet the Patriarch anytime, anywhere.

In a joint declaration, the two church leaders said: "We hope our meeting contributes to the re-establishment of this unity wished for by God."

They also issued a global appeal for the protection of Christians in the Middle East.

"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," they said in their joint declaration.

"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, the largest of the Orthodox Churches, since February 2009.

Pope Francis took up office in March 2013.