A profound price of the church's success was that security from persecution gave greater leeway for controversies to develop that led into factions that developed and that caused the propagation of heresies. But a benefit of having an emperor who professed to believe in Christianity was that the church was able to call an ecumenical (churchwide) council to debate the controversies and propound an orthodox position.

Gnosticism

Gnosticism was already extant when the church began, in the time of the Book of Acts. In general, Gnosticism believes in “secret knowledge,” which is akin to and sometimes overlaps occultism. It is dualistic, meaning it believes in virtually equal good and evil divinities, and that the good divinity rules the spirit, and the evil, the material realm. Orthodox Christianity professes, conversely, that in becoming a man in the form of Jesus Christ, God took on material form, and that in this, all of his creation was blessed and to be appreciated, not rejected. Some claim that despite Gnosticism's early origin, its best-known representation is in Dan Brown's contemporary novel, The Da Vinci Code.

Considering all the persecution of Christians in the church's first three centuries, the numbers of Gnostics were diminished by the fourth century, though there have been small groups of them throughout modern history. New Age philosophy, which had a resurgence in the late 1960s and 1970s, is widely considered a revival of Gnosticism, as was the emergence of theosophy (religious philosophy based on mystical insight into the divine), and other attempts to introduce Asian dualism (yin and yang) in western forms earlier in the nineteenth and twentieth centuries.

Though much of Gnostic writing is prescientific, some of its source material has been used in some of the “scientific” or humanist approaches to Christianity advocated by form criticism (analyzing the literary forms of biblical passages) and evolutionary theology.

Montanism

Montanus presented himself as a prophet from Phrygia, a province of Asia Minor (now Turkey) in the mid to late second century. He and his female disciples, prophetesses Prisca (Priscilla in English) and Maximillia, predicted an apocalypse in their time and claimed superiority over the church because they claimed to have received revelations directly from God. The Montanists taught that a convert who fell away from baptismal vows or beliefs could not be restored, though the church taught that repentance was always efficacious for any who lost the light and later returned to it.

Though the bishops of the church at the time counseled their followers to flee from persecution, Montanus and his followers advocated seeking out persecution. Part of the success of the sect was its tendency to exaggerate teachings that many others in the church also held, and eventually to dogmatize about their exaggerations. Orthodox believers in Asia Minor met in councils, and, after examining the Montanist teachings, condemned them and excommunicated their proponents. The sect died out, except in the immediate area of its origin, when its self-styled prophets died.

Manichaeism

Founded by Persian seer Mani in the third century, Manichaeism blended elements of all known religions at the time, especially Gnosticism, Christianity, and Zoroastrianism, under a strongly dualist umbrella. Mani is actually a title (something like “light king”), not a name, the name of the founder having been lost through the general use of his title. Mani claimed to have received a revelation from an angel of God at age twelve, and to have been told to wait another twelve years before launching his public ministry. This he did with this preamble: “As once Buddha came to India, Zoroaster to Persia, and Jesus to the lands of the West, so came in the present time this prophecy through me, the Mani, to the land of Babylonia.”

The sect is believed to have practiced forms of baptism and Eucharist. A Catholic source says that it's clear that Mani intended a convergence between his teachings and those of Christianity, which may have been the chief religion in Mesopotamia at the time he lived.

Mani is said to have rejected all of the Old Testament and adapted parts of the New Testament to suit his doctrines. In his dualism he regarded Jesus of Nazareth a fiction, and the true Jesus to be a personification of light. Like Gnosticism, Manichaeism taught that salvation comes through intellectual knowledge, and that ignorance is sin.

The sect spread rapidly beyond Babylon (or Mesopotamia) to India and other territories east of Persia, and throughout the Roman Empire, despite the persecution of its followers. In the Christian world, its strongest following was in Egypt, though it also had strong followings in Italy and seems to have penetrated to southern France, to the west of Rome, and to Bulgaria in the east.

Augustine (A.D. 354–430), the seminal theologian of the early church era among Roman Catholics and Protestants, and the bishop of Hippo on the North African coast (now Algeria), wrote against the Manicheans and described the extent of their heretical influence.

Donatism

After the persecutions of Emperor Diocletian described earlier, Donatus, a bishop of Carthage in North Africa (now Tunisia), refused to reinstate those who had renounced their baptisms to avoid martyrdom. He and other bishops he influenced said the sacraments of such “apostates” were invalid. He refused priests and bishops permission to serve sacraments in their sees, and also forbade their parishioners to receive sacraments from such when traveling.

A council in Arles, France, called by Emperor Constantine in 314 (just a year after his Edict of Milan) condemned the Donatists' refusal to forgive the repentant former apostates.

The Donatists refused to accept the council's decision and seceded from the rest of the church. Most of the churches in North Africa sided with the Donatists until Augustine's writing against the heresy won the majority back.

Arianism

The most important heresy and controversy in the early church was Arianism, as it forced the church to define the Trinity and hold its first Ecumenical Council. Arius (256–336), a priest in Alexandria, Egypt, taught that Christ, though divine, was not coeternal with God the Father, and was therefore inferior to him. His teaching was originally offered as an alternative to a less widespread heresy, Sabellianism or modalism, which held that the three persons of the Trinity were merely different modes of God's appearing or interacting, or roles he was using with his creation.

Arianism became popular in the church, and for some time it seemed to have won more support than the Trinitarians (who believed that the Father, Son, and Holy Ghost of the Trinity were equal parts of one Godhead), whose cause was most eloquently argued by Athanasius, also an Alexandrian, ordained a priest a little after Arius. Emperor Constantine called the first Ecumenical Council of the church in Nicea, just outside Constantinople, in 325 to settle the controversy. Athanasius accompanied Alexander, the bishop of Alexandria, a Trinitarian and the council's president, to the Council, and Athanasius emerged as the most persuasive speaker for the Trinitarian side.

The Council adopted Athanasius' position, and issued the original form of the Nicene Creed to define it. Though the Council had spoken, Arius' defenders continued campaigning against the Trinitarian position and persuaded Constantine to grant amnesty to the Arians who had been exiled after the Council and, instead, to exile Athanasius. By A.D. 360, another debate had broken out over the divinity of the Holy Spirit. After Constantine's death in 337, his successors were less interested in Christianity than he had been, until the succession of Theodosius I the Great in 378. He convened the second Ecumenical Council in Constantinople in 381 to finally settle the Arian/Trinitarian debates and to ratify the first Ecumenical Council.

Pelagianism

Pelagius, a monk who lived in Rome in the fifth century, taught that Adam's sin was not transferred to all human beings, and that salvation through works (in other words, keeping of the Old Testament Law) was possible without the work of Christ. Little is known about Pelagius, but Augustine said he lived a long time in Rome before he was excommunicated and exiled. Several regional church councils condemned his teachings, and the Ecumenical Council of Epheus ratified those condemnations in 431.

Nestorianism

Nestor, appointed patriarch of Constantinople by Theodosius II in 428, opposed the use of the term Theotokos to describe Mary, the Mother of Jesus. Theotokos is Greek, meaning “God-bearer,” and is usually rendered as “Mother of God” in English. Nestor's point was that while God was the Father of Jesus' divinity, Mary was the mother of only his humanity. This idea, however, separates Jesus into two distinct persons, which orthodox Christianity rejects. The Council of Ephesus was called in 431 to settle the controversy. The Council ruled that the Nicene Creed presupposes Mary's motherhood of both the divine and human natures (not persons) of Jesus by affirming that no separation is possible between his godhead and his manhood.