The Byzantine Church, or Orthodox Church as it was later called, gradually affirmed its differences in respect to a number of practices and interpretations. On practices, the most important differences related to priestly celibacy, which it rejected (see hereinafter), as well as the bread consecrated for the Eucharist: the Latin Church used unleavened bread in continuation of the Jewish tradition, while the Orthodox Churches, to mark the break with Judaism, used leavened bread. On a doctrinal level, the Byzantine Church rejected the interpolation of the Filioque phrase in the statement of creed. The Niceno-Constantinopolitan Creed proclaimed that the Holy Spirit proceeds from the Father (ex Patre procedit), whereas the Churches of several Western Kingdoms, in order to reaffirm the divinity of Jesus over heresies which denied it, added that the Spirit also proceeds from the Son (ex Patre Filioque procedit). The Pope consented to its inclusion in 1014. For the Byzantine Church, the Creed could not be altered without the consent of an ecumenical council; further, the Filioque underestimated the Holy Spirit in the Trinity. Conversely, the Latin Church considered that rejection of the Filioque underestimated the divinity of Jesus.
In addition, the iconoclastic crisis led the Byzantine Church to develop a theology of icons that was unsettling to a Latin church instilled with the idea of Gregory I (590-604) that images were "the book of the illiterate", thereby not giving them similar importance. The Byzantine emperors Leo III (r. 717-741) and Constantine V (r. 741-775) opposed the veneration of images of saints, which had gained in popularity, and they carried out a policy to destroy icons, considered a sign of idolatry. In 787, the Second Council of Nicaea reinstated their veneration, but a second iconoclastic period began in 815. In 843, the controversy was finally settled, and the use of icons was restored on the first Sunday of Lent, commemorated since as the Sunday of Orthodoxy in the Eastern Churches. The iconostasis replaced the chancel screen between the nave and the sanctuary, placing the veneration of icons at the center of Orthodox liturgy.
The Byzantine Church also claimed its difference in reaction to changes in the Latin Church. It was opposed to priestly celibacy as was being imposed in Latin Christendom, holding that only monks and bishops were bound to celibacy. One of the most important disputes between the two Churches involved the place of the Pope. The Council of Chalcedon (451) created five patriarchates: Rome, Constantinople, Alexandria, Antioch and Jerusalem, in hierarchical order. For the Orthodox, this hierarchy was purely honorary and the Church was based on cooperation between the five patriarchs. However, the Pope believed that the primacy of Rome was real, which placed him at the head of Christendom. This led, in the West, to the assertion of Roman authority over all state Churches. In the East, the other patriarchs refused to submit to the supremacy of the Pope.
The Byzantine Church’s claim to specificity hence carried with it a conflict with Rome. The extent to which the relationship was strained depended on the times, but it led to the separation of Christendom between the Latin (Roman Catholic) and the Byzantine (Orthodox) Churches. The first step in this separation occurred during the iconoclastic crisis. When the controversy began, Pope Gregory II (r. 715-731) rejected iconoclasm, and his successors continued in this direction. In that time, the Lombards had also increased their incursions into Byzantine Italy: after the fall of Ravenna (751), Rome was threatened. Zachary (r. 741-752) and Stephen II (r. 752-757) turned to the Frankish King Pepin the Short (r. 751-768), whose expeditions into Italy led to the creation of the Papal States: Rome was taken out of the Empire, but it stayed in communion with Constantinople once the iconoclastic crisis was settled.
From the 9th century, the conversion of the Slavs brought on a new confrontation. In Bulgaria, Latin and Byzantine missionaries found themselves in contention, a situation which brought out divergences in their practice. This embittered the conflict between Pope Nicolas I (r. 858-867), who presumed to intervene in the affairs of the Patriarchate of Constantinople in the name of the Roman primacy, and the Patriarch Photios (r. 858-867 and 877-886), who rejected Roman jurisdiction while recognizing an honorary primacy in the Pope.
Tensions between Rome and Constantinople lead to the East-West Schism of 1054, which is the date traditionally ascribed to the division of Christianity into its Latin and Byzantine branches. Mutual excommunications by the Patriarch of Constantinople and papal legates in 1054 marked the climax of a serious crisis, but they did not signify at that point the separation of the Latin and Byzantine Churches. Relations remained cordial enough that Urban II (1088-1099), at the Council of Clermont (1095) and in response to an appeal by the Byzantine emperor, urged Christians of the West to rescue the eastern Churches from the Turkish advance.
The Crusades were the real cause of the separation of the Latin and Byzantine Churches. The Byzantine Church was hostile to the idea of a holy war. The Empire intended to use crusaders to recover territories recently conquered by the Turks, but after the Principality of Antioch was founded (1098), it became clear that the crusaders had other objectives. After the First Crusade (1095-1099), the Latins continued to criticize the Byzantines, whom they felt were not supporting them strongly enough against the Muslims. The divide lasted until the Fourth Crusade (1198-1204), which ended with the capture of Constantinople and the creation of new Latin Empire states on former Byzantine territory. For the Latins, it was an opportunity to bring under Roman authority a Byzantine Church that was in error; for the Byzantines, it was a betrayal that revealed the barbarous and pernicious nature of the Latin crusaders who were Christian in name only.
Nevertheless the break was not final, and there followed several attempts to restore the communion. After extended negotiations, the union of the Eastern and Western Churches was proclaimed a first time at the Second Council of Lyon (1272-1274), and again at the Council of Ferrara-Florence (1438-1439). Each time, however, the agreements were rejected by a substantial constituency of the Byzantine Church, for what they regarded as concessions pledged by the Emperor and imposed on them in return for Latin military support.