With the recent death of its long-time spiritual leader and the increasing political power of Islamists, Egypt's Christian community is faced with one of its toughest challenges.
Pope Shenouda III died on March 17 after 40 years at the helm of one of the world's most ancient denominations, the Orthodox Coptic Church. His death at the age of 88 led to an outpouring of grief among the estimated 10 million Christians in Egypt, with tens of thousands flocking to the church's main cathedral in Cairo for his funeral and to his burial ceremony at a desert monastery.
The country's military ruler, Field Marshal Hussein Tantawi, declared a state of mourning on the day of the burial and the nation's top Muslim clerics offered their condolences in person to the black-clad clergy of the church.
Muslims spoke in positive terms of Egypt's national unity and how Muslims and Christians were united in their love for their country.
Some newspapers found evidence of that harmony between the religions communities in the image of a woman wearing the Muslim headscarf offering water to the Copts who waited for hours outside the cathedral to pay their final respects.
The woman, seen at her apartment's balcony, lowered the water bottles in a wicker basket to the Christians below.
That act of kindness, though symbolic, might be of little consolation to some Christians.
Egypt's Christians have long complained of discrimination. Christians, for example, rarely assume top jobs in the police force, particularly the security agencies, and government cabinets never included more than one or two Christians.
As Egypt grew more religiously conservative over the past 50 years, the discrimination became more obvious. Christians often faced long delays when seeking government documents, particularly if they were requesting permits to build or repair churches. Christian children attending state-run schools, where Islamists often dominate the staff, complained of discrimination by teachers and isolation when they have to leave their classrooms during religion studies.
A series of attacks over the last year has also stoked Christian fears. A year ago, a Muslim-Christian love affair led a Muslim mob to torch a church in the village of Soul, 30 kilometres south of Cairo. Christians protesting the burning were attacked by a mob; 13 people died and 140 injured. In May, ultraconservative followers of the Salafi trend of Islam burnt a church in the Cairo working-class district of Imbaba and clashed with Christians, leaving 12 people dead.
Many of the rioters believed that a Christian woman who fell in love with a Muslim man had converted to Islam and was being held prisoner by the church. In October, a Cairo protest led by Copts demanding greater rights was crushed by soldiers, leaving 27 people, mostly Copts, dead.
Islamists, including the relatively moderate Muslim Brotherhood, dominated the elections held late last year. The Salafis won about 25 per cent of the seats in the People's Assembly - parliament's lower house.
In a move that speaks of how some Salafis view Copts, many of their MPs walked out of the chamber last week when the speaker, Saad El Katatni, asked members to stand and observe a minute of silence to mark the death of Shenouda. Those Salafis who stayed behind remained seated.
The more pragmatic Muslim Brotherhood, unlike the Salafis, consistently make the right noises about the Christians. But liberal and leftist Egyptians say they only offer symbolic gestures, such as leaders frequently calling on the church's leadership for "political consultations" and praising Shenouda after his death.
Regardless of the intentions of the Muslim Brotherhood and the Salafis, the fact that Egypt is falling under the control of the Islamists concerns Christians.
For it to happen when the church has lost its seasoned protector is a double blow to the community, whose leaders have spoken in recent months about higher-than-usual number of Christians permanently leaving the country.
Shenouda supported Mr Mubarak during his 29 years in power in return for the former president's protection of the community from the Islamists. The patriarch's delicate balancing act entailed never appearing angry or emotional in public when the going was rough for Christians, and keeping communications open with the regime and Muslim religious leaders. Shenouda had, on occasion, protested against the more serious injustices to his flock by living in seclusion for days or even weeks in remote monasteries.
The St Bishoy Monastery in the desert, where Pope Shenouda has been laid to rest, is where he stayed when Mr Mubarak's predecessor, Anwar Sadat, banished him in 1981 for allegedly fomenting unrest. He stayed there more than three years until Mr Mubarak ordered his release.
With additional reporting by the Associated Press