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Egypt also hosts two major religious institutions. Al-Azhar University, the oldest Islamic institution for higher studies (founded around 970 CE) with its corresponding mosque Al-Azhar. The head of Al-Azhar is traditionally regarded as the supreme leader of Sunni Muslims all over the world. Egypt also has a strong Christian heritage as evidenced by the existence of the Coptic Orthodox Church headed by the Patriarch of Alexandria, which claims a following of 50 million Christians worldwide (one of the famous Coptic Orthodox Churches is Saint Takla Haimanot Church in Alexandria

Despite the political upheaval, Egypt remained a predominently Christian land, although gradual conversions to Islam over the centuries had the effect of changing Egypt from a predominantly Christian to a predominantly Muslim country by the end of the 12th century.

Islam in Egypt came to the country with the successors of Mohammed, and is today the dominant faith with 90% of the population adherents, almost all of the Sunni denomination

Under Islam, Egypt continued to be a great source of literary endeavour, now in the Arabic language. In 970, al-Azhar University was founded in Cairo, which to this day remains the most important centre of Sunni Islamic learning. In the 12th century Egypt, the Jewish talmudic scholar Maimonides produced his most important work.

The President names the Prime Minister and may preside over the cabinet. President Mubarak holds a monthly meeting with the cabinet on which he presides. In addition, the President is the Supreme Commander of the Egyptian Armed Forces. The President concludes treaties and may submit questions to national referenda. The President also possesses the constitutional power to dissolve the People’s Assembly, however, no President has ever done so. In certain emergencies, the President may assume special, comprehensive powers.

Islamists rejected Marxism and Western capitalism. Indeed, they viewed atheistic communism, Jewish Zionism, and Western "Crusader-minded" Christianity as their main enemies, which were responsible for the decadence that led to foreign domination and defeat by Zionists. They were intolerant of people who did not share their worldview. Islamists tended to be hostile toward the orthodox ulama, especially the scholars at Al Azhar who frequently criticized the Islamists' extreme religious interpretations. Islamists believed that the established social and political order had tainted the ulama, who had come to represent stumbling blocks to the new Islamic order. In addition, Islamists condemned the orthodox as "pulpit parrots" committed to a formalist practice of Islam but not to its spirit.

The Muslim Brotherhood's reemergence as a political force coincided with the proliferation of Islamic groups. Some of these groups espoused the violent overthrow of the government while others espoused living a devout life of rigorous observance of religious practices. It is impossible to list all the Islamic groups that emerged in the late 1970s because many of them had diffuse structures and some of the more militant groups were underground. Egypt's defeat and loss of territory in the June 1967 Six-Day War was the main cause for the growth of religiously inspired political activism. Muslims tended to view the humiliating experience as the culmination of 150 years of foreign intrusion and an affront to their vision of a true Islamic community. Islamic tradition rejected the idea of non-Muslims dominating Muslim society. Such a state of affairs discredited Muslim rulers who permitted it to persist. It was, therefore, incumbent on believers to end the domination and restore the true supremacy of Islam. As part of their Sunni creed, the most radical activists adopted jihad and committed themselves to battling unbelievers and impious Muslims. During the 1970s and 1980s, Islamists perpetrated a number of violent acts, including the assassination of Anwar Sadat in October 1981.

The current Coptic Orthodox Pope of Alexandria and the Patriarch of the Holy See of Saint Mark is Pope Shenouda III; the most recent Greek Orthodox Melkite Patriarch is Patriarch Theodoros II. These positions should not to be confused with that of the Roman Catholic Pope in Rome, nor with either of the other two bishops bearing the title of Patriarch of Alexandria (one in communion with the Roman Pope and the other the head of one of the canonical Eastern Orthodox churches).

After the 1952 Revolution, the government assumed responsibility for appointing officials to mosques and religious schools. The government mandated reform of Al-Azhar University beginning in 1961. These reforms permitted department heads to be drawn from outside the ranks of the traditionally trained orthodox ulama.