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.