The Copts have remained a significant minority throughout the medieval and modern periods. After the Turks incorporated Egypt into the Ottoman Empire in the sixteenth century, they organized the government around a system of millets, or religious communities. The Copts were one of the communities. Each organized religious minority lived according to its own canon law under the leadership of recognized religious authorities who represented the millet to the outside world and supervised the millet's internal communal life. This form of organization preserved and nourished the religious differences among these peoples. Most historians believe that the millet system prevented the full integration of non-Muslims into Muslim life. The system, which the Ottomans applied throughout their empire, had an enduring influence on the social structure of all countries in the Middle East.

The Copts, an indigenous Christian sect, constituted Egypt's largest religious minority. Estimates of their numbers in 1990 ranged between 3 million to 7 million. The Copts claimed descent from the ancient Egyptians the word copt is derived from the Arabic word qubt (Egyptian). Egypt was Christianized during the first century A.D., when the country was part of the Roman Empire. The Coptic Church claims to hold an unbroken line of patriarchal succession to the See of Alexandria founded by Saint Mark, a disciple of Christ. Egyptian Christianity developed distinct dogmas and practices during the more than two centuries that the religion was illegal. By the fourth century, when Constantine made Christianity the official religion of the Roman Empire, Coptic traditions were sufficiently different from those in Rome and Constantinople (formerly Byzantium present-day Istanbul) to cause major religious conflicts. Dissension persisted for 150 years until most Copts seceded from the main body of Christianity because they rejected the decision of the Council of Chalcedon that Christ had a dual nature, both human and divine, believing instead in Christ's single, divine nature.

The Coptic Church developed separately from other Eastern churches. The Coptic Church's clerical hierarchy had evolved by the sixth century. A patriarch, referred to as the pope, heads the church. A synod or council of senior priests (people who have attained the status of bishops) is responsible for electing or removing popes. Members of the Coptic Church worldwide (about 1 million Copts lived outside of Egypt as of 1990) recognize the pope as their spiritual leader. The pope, traditionally based in Alexandria, also serves as the chief administrator of the church. The administrator's functionaries includes hundreds of priests serving urban and rural parishes, friars in monasteries, and nuns in convents.

Following Islam's spread through Egypt, Muslims alternately tolerated and persecuted the Copts. Heavy taxation of Christians encouraged mass conversions to Islam, and within two centuries, Copts had become a distinct minority. By the tenth century, Arabic had replaced Coptic as the primary spoken language, and Coptic was relegaf0f gated to a liturgical language.

The Ottoman millet system of drawing administrative divisions along religious lines reinforced Coptic solidarity. The dismantling of the millet system during the nineteenth century helped open new career opportunities for the Copts. Egypt's Muslim rulers had traditionally used minorities as administrators, and the Copts were initially the main beneficiaries of the burgeoning civil service. During the early twentieth century, however, the British purged many Copts from the bureaucracy. The Copts resented this policy, but it accelerated their entry into professional careers.

In the twentieth century, Copts have been disproportionately represented among the ranks of prosperous city dwellers. Urban Copts tended to favor careers in commerce and the professions, whereas the livelihoods of rural Copts were virtually indistinguishable from their Muslim counterparts. Urban Copts were stratified into groups of long-time residents and groups of recent migrants from the countryside. The latter group was often impoverished and fell outside the traditional urban Coptic community. The former group included many university professors, lawyers, doctors, a few prominent public officials, and a substantial middle echelon of factory workers and service sector employees.

Anti-Coptic sentiment has accompanied the resurgence of Islamic activism in Egypt. Since 1972 several Coptic churches have been burned, including the historic Qasriyat ar Rihan Church in Cairo. Islamist groups frequently and explicitly denounced Copts in their pamphlets and prayer meetings. The increasing tensions between Copts and Muslims inevitably led to clashes in Upper Egypt in 1977 and 1978 and later in the cities and villages of the Delta. Three days of religious riots in Cairo in 1981 left at least 17 Copts and Muslims dead and more than 100 injured. Isolated incidents of Muslim-Coptic violence continued throughout the 1980s and during 1990.

Coptic Pope Shenudah III (elected in 1971) blamed government silence for the increasing violence. He also expressed alarm at official actions that he said encouraged anti-Coptic feelings. In 1977, to protest a Ministry of Justice proposal to apply sharia legal penalties to any Muslim who converted from Islam, the pope called on the Coptic community to fast for five days. As harassment of Copts increased, Pope Shenudah III canceled official Easter celebrations for 1980 and fled to a desert convent with his bishops. Sadat accused the pope of inciting the Coptic-Muslim strife and banished him in September 1981 to internal exile. The government then appointed a committee of five bishops to administer the church. The following year, the government called upon the church synod to elect a new pope, but the Coptic clergy rejected this state intervention. In 1985 Husni Mubarak released Pope Shenudah III from internal exile and permitted him to resume his religious duties.

Data as of December 1990