The meeting later this month in Crete will be convened by Ecumenical Patriarch Bartholomew I, the Istanbul-based spiritual leader of the world's 300 million Orthodox Christians.
All the Orthodox churches, old and new that emerged over the centuries, have never met like this before - not since the "great schism" of 1054, when the Orthodox and Roman Catholics split after disputes over the Vatican's power.
Bartholomew's spokesman, the Rev. John Chryssavgis, told The Associated Press that the June 19-26 gathering's "sole purpose is the affirmation of unity."
"Unity is a slow and painful process. We don't have to be united on every point to convene the council; but we do have to convene the council if we aspire to unity," Chryssavgis said.
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The call followed reports that the Bulgarian Orthodox Church, which is due to come to Crete, had threatened to pull out, reportedly asking for some mostly procedural changes to the agenda. It did not say what changes it was requesting or if it would carry out the threat.
"It is very natural, then, for some Churches to feel unsure or uncomfortable about coming together after such a long time, much like members of a family might be skeptical and even mistrustful after a long period of separation," he said.
Unlike the Roman Catholics, the Orthodox churches are independent and have their own leadership. For example, Patriarch Kirill of Moscow is head of the world's largest Orthodox Church, but is considered equal to other patriarchs. Bartholomew is called the "first among equals," but leads a smaller flock than Kirill.