Pope Shenouda III is the president of the Holy Synod, which is the highest body in the Coptic Church. The Holy Synod is made up of all the Church’s bishops. It assembles annually on the Saturday prior to the Pentecost Sunday. In 1985, Pope Shenouda established seven committees of the members of the Holy Synod and entrusted them with the tasks of the ecumenical relations, monastic affairs, pastoral affairs, and ethics, liturgy, and deacon affairs. Pope Shenouda divided the large dioceses into a number of small ones and founded many new dioceses to facilitate the work of the bishops in guiding their communities.

He consecrated a number of extradiocesan bishops for several affairs such as public, social, and ecumenical services. Many bishops had been ordained to serve hundreds of thousands of Copts in the United States, Canada, Australia, and Europe, in addition to the Coptic Orthodox communities in Africa. Coptic monasteries provided the Church with the educated new bishops.

The following are the Coptic dioceses of Lower Egypt: Dimyat and Kafr al-Sheikh and the Monastery of St. Demyana, Damanhur and Behira and Pentapolis, Minufiya, Benha and Qwisna, Tanta, Sharqyia, Zaqaziq and Minya al-Qamh, Mansura, Port Said, Isma‘ilia, Suez, and Horgada.

Sinai: Al-Arish and North Sinai, al-Tur and South Sinai.

Upper Egypt: Giza, Fayoum, Beni Suef, Beni Mazar and al-Bahnasa, Biba and al-Fashn, Maghagha and Idwa, Samalout, Abu Qurqas, Minya, Dayr Mawwas, Matai, Malawi, Dayrut and Sanabu, Qusia and Mer, Assiut, Manfalout, Abnub, Abu Tig and Sidfa, Tima, Tahta, Sohag, Akhmim and Saqulta, Girga, Baliana, Nag‘ Hammadi, Dishna, Qena and Qift, Naqqada and Qus, Luxor and and Esna, and Aswan

The patriarch of the Coptic Church is traditionally the Bishop of Alexandria and Cairo. However, Pope Shenouda also consecrated “general” bishops for some districts belonging to Greater Cairo in Halwan and Ma‘sara, Ma‘adi and Dar al-Salam, al-Khema, East Cairo, and Shebine al-Qanater and al-Khanka, and Old Cairo. There are also a number of general bishops, such as the bishop for youth affairs, and the bishop for African affairs. Outside of Egypt are the following: Jerusalem, Stevenage (U.K.), Scotland, Ireland, and East England (U.K.), Birmingham (U.K.), Glastonbury (U.K.), Hoxter-Brenkhausen (Germany), Vienna (Austria), Toulon (France), Marseilles (France), Rome (Italy), Milan (Italy), Melbourne (Australia), Sidney (Australia), Los Angeles (U.S.), Colleyville (U.S.), New Jersey (U.S.), Khartoum (Sudan), Atbara and Um-Durman (Sudan).

The abbots of the following monasteries are bishops residing in their monasteries: the Monastery of Patmus, the Monastery of St. Samuel (al-Qalamun), the Monastery of al-Baramous, the , Abu Mina (the Monastery of St. Menas), the Monastery of St. Pschoi, al-Muharraq (Monastery of the Holy Virgin Mary), the Monastery of St. Antony, and Dayr Mari Girgis at Khatatba. The following monasteries are also populated: the Monastery of St. Macarius, the Monastery of St. Paul, the Monastery of the Gabriel at Naqlun, the Monastery of St. George at Sedment, the Monastery of St. Shenute, the Monastery of St. Thomas, the Monastery of St. Michael (al-Malak), the Monastery of the Martyrs, the Monastery of the Holy Virgin, the Monastery of St. George, and the Monastery of St. Psote.

The previous six monasteries are in the region of Akhmim the Monastery of St. Palamoun (Nag Hammadi), the Monastery of St. Pachomius (Luxor), the Monastery of St. George (al-Riziqat), the Monastery of the Potter (Esna), and the Monastery of St. Pachomius (Edfu).

Although the Coptic Church is a monastic organization as its patriarch and all its bishops are chosen from among the monks, the laymen play a considerable role in its activities in Egypt as well as in the Diaspora. The participation of women in these activities has remarkably improved in the past few decades.