The main purpose of the visit is to meet Patriarch Bartholomew, the head of the world's 250 million Orthodox Christians.
Archbishop Demetrios, primate of the Greek Orthodox church in America, said that the pope's visit would be about promoting diversity and untiy between the Christian Orthodox church and the Christian Catholic church and to promote unity between all religions.
Demetrios said he hoped scheduled talks between the pope and the patriarch in Istanbul "might help improve conditions" for the patriarchate.
He said the major issues were Turkey's refusal to recognise patriarch Batholomew as the leader of the Orthodox church across the world and grant his patriarchate legal status.
The ecumenical patriarchate in Istanbul dates from the Greek Orthodox Byzantine empire, which collapsed in 1453.
On Tuesday, the Orthodox church in Turkey said that it hoped the pope's visit would help convince the Turkish government to enhance the status and rights of its followers.
It is expected that the pope will also talk about the legal rights of the Catholic church, along with other minorities, in Turkey.
Over the course of the trip, the pope is also expected to visit the mausoleum of Mustafa Kemal Ataturk, secular Turkey's founding father, in Ankara, as well as the Blue Mosque and the Aya Sofya (Hagia Sophia) in Istanbul.
The pope has said that this "is not a political visit".
Turkish security teams took up positions earlier on Tuesday around Istanbul and Ankara. The authorities say security will be tighter than it was when George Bush, the US president, visited in 2004.
"The majority of the Turkish people welcome the pope on his visit"
Doctor Sinasi Gunduz, professor in Islamic theology
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Barnaby Phillips, Al Jazeera's correspondent in Turkey, reported: "In Istanbul there are gangs of policemen on almost every street corner. There is talk of decoy convoys and bulletproof limousines. The Turkish authorities are clearly going the extra mile."
He said: "The pope will have to tread and speak very carefully over the next four days."
Ismail Caliskan, a police spokesman in Istanbul, said: "We have taken all the necessary measures and observations of the route the pope [will travel] and the places the pope will visit."
Pope Benedict is to travel through the streets of Ankara and Istanbul in an armoured car rather than the glass-sided "pope mobile" traditionally used on papal trips.
The Turkish authorities have said they will impose a security clampdown on the House of the Virgin Mary, in close to Ephesus, where the pope will celebrate mass on Wednesday.
Protests over visit
The visit is the first to a predominantly Muslim country for the pope and there were large protests ahead of it.
More than 20,000 people rallied on Sunday in Istanbul, chanting "Pope don't come."
The Turkish government says the protests have been small and staged by a minority.
Doctor Sinasi Gunduz, a professor in Islamic theology, told Al Jazeera: "The majority of the Turkish people welcome the pope on his visit, but they expect him to say that Islam is a peaceful religion that has contributed a great deal to human history."
The protests have focused on comments he has made about Islam.
Security is said to be tighter than it was
for the US President's visit in 2004
In September, the Pope delivered a lecture where he quoted a Byzantine emperor. The lecture was widely interpreted as portraying Islam as a religion coloured by violence.
Thousands of Muslims held protests around the world demanding he apologise. The pope later expressed regret over the pain his remarks caused, but stopped short of a full apology.
Turkey is also sensitive to criticism over its bid for membership of the EU. Although the Vatican has said it does not oppose EU membership for Turkey, the pope expressed reservations over the country's bid to join the union when he was a cardinal.
Patriarch Bartholomew has said he will tell Pope Benedict that the EU must not be a "Christian club" and that Turkey must be allowed to join.