The early period of the Christian church was troubled by a number of dissensions about the nature and relationship of the three Persons of the Trinity. In the West the Holy Spirit was seen as coming from the Father and the Son, though subordinate to neither. In the Eastern part of the (as yet) undivided Catholic church the spirit was seen as originating from the Father alone, although the Son sent the Holy Spirit under the title paraclete. The phrase and the son, (in Latin, filioque), was first added to the Nicene Creed at the Synod of Toledo in Spain in 447. The formula was used in a letter from Pope Leo I to the members of that synod, responding to heresies they were confronting. At the third synod of Toledo in 589, the ruling Visigoths, who had been Arian Christians submitted to the Catholic Church and were obliged to accept the Nicene Creed with the filioque. The Eastern Orthodox churches refused to accept a formula which they saw as an innovation in doctrine.

Further, although the second Ecumenical Council had amended the Nicene Creed, the third Ecumenical Council, the Council of Ephesus in 431, had forbidden any further changes to it. In the ninth century, Pope Leo III agreed to the filioque clause theologically, but was opposed to adapting it in worship in Rome, and insisted on using the Nicene Creed in Mass in Rome as it was expressed at the Council of Ephesus and all the Ecumenical Councils up until that time. The dispute, though it had not caused the severance of communion over a 600 year period, contributed to the Great Schism of the Eastern and Western branches in 1054. In addition to the actual difference in wording and doctrine, a related issue was the right of the Pope to unilaterally make a change to the Nicene Creed, as opposed to having an Ecumenical Council define the Creed.

Some historians have suggested that the Franks may have pressured the Pope to adopt the filioque clause in order to drive a wedge between the Roman church and the other patriarchates. At least one pope refused to do so in the 800s because of doctrinal issues, and instead sought to make the Nicene-Constantinopolitan Creed (Nicene Creed as modified in 381) more prominent. A similar test of the Roman pope's supremacy came in the ninth century when there was some dispute as to whether Photius or Ignatius was Patriarch of Constantinople. The Pope of Rome unilaterally put forth Ignatius as Patriarch on his own authority and claimed to have deposed Photius. Photius's response included citation of the filioque as proof that Rome had a habit of overstepping its boundaries.

The Roman Catholic Church has not proved unwilling to negotiate on the topic. The Eastern-rite churches of the Catholic Church -- who include the Maronites, the Melkites, the Ruthenians -- returned to union with the Papacy at various dates but were not required to say the "and the Son" formula in their liturgies. However, they are still required to teach the underlying doctrine. This may also suggest that filioque clause dispute is merely a symptom of the larger dispute concerning papal authority.

Dialogue on this and other subjects is continuing. The filioque clause was the main subject discussed at the 62nd meeting of the North American Orthodox-Catholic Theological Consultation, which met at Hellenic College/Holy Cross Greek Orthodox School of Theology June 3-5, 2002, for their spring session. As a result of these modern discussions, it has been suggested that the Orthodox could accept an "economic" filioque that states that the Holy Spirit came "through the Son", but this has not been universally accepted in the Orthodox Church.