Christianity arrived in Egypt from Judea, possibly as early as the 1st century AD. It probably first came into Alexandria, which was both an intellectual centre and the home of a large Jewish community. Christianity was heavily persecuted during the reign of the emperor Diocletian in the 3rd century AD, and many Christians were martyred. One famous martyr was Saint Menas whose tomb in the desert west of Alexandria became the focal point of pilgrimages throughout the medieval period.

However, when Christianity became the official religion of the Empire during the 4th century AD, it spread rapidly through Egypt. These early Christians were often attracted to the Egyptian deserts, where they could live as hermits. Sometimes ancient rock tombs were adapted into dwellings and impressive monasteries were built to house communities of monks.

Egyptian Christianity suffered a number of divisions, the first of which centred on the so-called Arian heresy which stressed the human aspect of Christ. A similar belief, known as the Monophysitic error, was put forward by the Patriarch of Alexandria in the 5th century. At the Council of Chalcedon in 451 this doctrine was rejected, and the Egyptian Church separated from the main body of the Christian Church.