Christians gathered today to pay final respects to Pope Shenouda III, who sought to soothe sectarian tension in his four decades atop Egypt's Orthodox Church.
Friction between the sides has worsened since former president Hosni Mubarak, who suppressed Islamists, was ousted last year with increasing flare-ups in the majority Muslim nation.
Pope Shenouda, who died yesterday aged 88, often called for harmony and regularly met Muslim and other leaders.
Christians, who comprise about a tenth of Egypt's 80 million people, have long complained of discrimination and in the past year stepped up protests, which included calls for new rules that would make it as easy to build a church as a mosque.
Pope Shenouda had served as the 117th Pope of Alexandria since November 1971, leading the Orthodox community who make up most of Egypt's Christians. His funeral will be held on Tuesday, Egyptian state media reported.
US president Barack Obama offered his condolences and Pope Benedict, leader of the world's Roman Catholics, offered prayers after being informed of his death.
"I would like to express to the members of the Holy Synod, to the priests and to the faithful of the Patriarchy, my strongest feelings of fraternal compassion," said Benedict.
Describing Pope Shenouda as a long-time advocate of unity among Christians, he said the Catholic Church "shares the pain afflicting Orthodox Copts.
"Thousands of Christians queued in Cairo's Abbasiya district overnight and on Sunday morning at the cathedral where his body was initially laid in a coffin and later seated on a ceremonial throne wearing gold and red embroidered religious vestments, a golden mitre on his head and holding a gold-topped staff.
He was popular among many of Egypt's Christians even outside the Orthodox Church, as well as among many Muslims.
However, some Christian activists said he should have pushed the state harder to secure more rights for Christians.
In one phrase he often repeated and which was also cited in newspapers, he would say: "Egypt is not a nation we live in, rather it is a nation that lives in us."
The burial is expected to take place at the Wadi el Natrun monastery in the desert northwest of Cairo, where the late pope had requested he be buried.
Pope Shenouda was banished to Wadi el Natrun monastery in 1981 by then-resident Anwar Sadat after he criticised the government's handling of an Islamic insurgency in the 1970s and Egypt's 1979 peace treaty with Israel.
Reuters