Autocephaly (from Greek "self-headed") is the status of a hierarchical Christian church whose head bishop, while still in full communion with the church, does not report to any higher-ranking bishop. The religions with autocephaly are 
and all of its heresies except Bogomilism; 
and its heresy Monophysite. With 
Holy Fury, reformed pagan faiths with the Autocephalous leadership type also have this mechanic.
The religion still has an overall religious head, but they are less powerful than other religious heads, as they delegate some powers to the autocephalous patriarchs in the latter's jurisdiction.
The heads of religions can be split into two types: pentarchs and autocephalous patriarchs. The former's influence is based on tradition, while the latter is more de facto.
Pentarchs
The five historical pentarchs (baron-tier bishops of the historical episcopal sees) will always act as autocephalous patriarch of rulers in their respective de jure kingdom and other associated kingdoms:
- Patriarchate of Rome: Kingdoms of Italy, Aquitaine, Aragon, Asturias, Bavaria, Burgundy, England, France, Frisia, Germany, Ireland, León (only after 20 December 910), Lotharingia, Naples, Navarra, Portugal and Sicily
- Patriarchate of Constantinople: Kingdoms of Greece and Anatolia
- Patriarchate of Jerusalem: Kingdoms of Jerusalem and Arabia
- Patriarchate of Antioch: Kingdoms of Syria, Armenia and Mesopotamia
- Patriarchate of Alexandria: Kingdoms of Egypt, Abyssinia, Africa and Nubia
Religious heads of religions which use autocephaly will also hold one of these Pentarch positions, but these are separate positions that happen to have the same person holding them. They will gain the appropriate pentarch if the following is true:
- The pentarch title is held by the appropriate religion
- Any liege is of high enough tier to vassalize them
Once this is met, the patriarch usurps the pentarchy title and becomes the vassal of the lowest-tier liege that can support them. The top liege being of the appropriate religion is not a requirement, leading to such hilarity as the Coptic Pope being a vassal of the Sunni Sultan of Egypt and the Sunni Caliph of Arabia.
Below is a brief list of religious heads using Pentarchy mechanics and the Pentarch seat they will usurp:
- The Ecumenical Patriarch (Constantinople)
- The Monotheilite Patriarch (Antioch)
- The Paulician Patriarch (Constantinople)
- The Iconoclast Patriarch (Constantinople, if formed)
- The Coptic Pope (Alexandria)
- The Monophysite Patriarch (Alexandria)
- The Patriarch of the East (Antioch)
Autocephalous patriarchs
If a kingdom or empire of a religion with autocephaly does not have an associated pentarch (see above), the ruler of the realm will appoint a Court Chaplain that acts as the autonomous head of religion in the realm: the autocephalous patriarch.
If a kingdom or empire of a religion with autocephaly does have an associated pentarch but the de facto realm is larger than the de jure title, the aforementioned autocephalous patriarch only has jurisdiction over those provinces that lie within the realm but outside the de jure territory. For example, the Empire of Francia has most of its territory in the territory of the Bishopric of Rome, except for the territory of the de jure Kingdom of Brittany. In this event, the Patriarch of Francia is created and has jurisdiction over the Kingdom of Brittany.
The autocephalous patriarch has the ability to grant divorces and excommunication on characters with the same head. However, only the overall head may grant the Invasion Casus Belli. Even then, invasion is only allowed for those under the same patriarch.
Anyone who doesn't belong to the jurisdiction of an autocephalous patriarch will depend directly on the overall head for religious matters.
The jurisdiction of each autocephalous patriarch can be seen while the religious tab (not the religious map) is active.
Example
If we apply this to the Orthodox religion in 1066 (example on the right):
- The kingdom of Armenia is associated with the pentarch of Antioch. Since both titles exist, the nobles in the de jure territory of Armenia have Antioch as their religious head. The same applies to the kingdoms of Anatolia and Greece, whose de jure territories go to the pentarch of Constantinople (who is also the Ecumenical Patriarch, in usual cases).
- The kingdom of Georgia is not associated with any of the pentarchs. Its religious head, therefore, is the court chaplain of the king who becomes an autocephalous patriarch.
- All orthodox territory not yet assigned goes to the ecumenical patriarch (who happens to be the pentarch of Constantinople, but these are entirely different functions assigned to the same person).
Strategy
Having a vassal Patriarch is similar to having a vassal Antipope - he does just about anything you ask, and can excommunicate people and grant divorces. This means you can, at the cost of only a small amount of Piety, have a valid reason to imprison/declare war on any vassals, courtiers, and other rulers that are located in your Patriach's de jure kingdom and other associated kingdom.
Having multiple Pentarchs is a problem, as you must have the same religious head to request excommunications. In addition, you can't get Invasions between different patriarchs. Unlike Catholicism, you do not have Investiture (Free or Papal). Therefore, you cannot elect Pentarchs or the Ecumenical Patriarch (or other appropriate religious heads). However, as autocephalous Patriarchs are your Chaplain, you can "elect" a good Patriarch by choosing a good Court Chaplain.