The Picts were a profoundly religious people. Like all Celts they worshipped an unknowable god, represented by the sun who was seen as the giver of light, of bountiful harvests, of warmth and good health. The precise astronomical alignment of the giant stone circles that were a fundamental part of their worship, are testimony not only to their faith but to their knowledge of mathematics, geometry, surveying and the calendar.

St. Columba, related to the High Kings of Ireland, became a Christian missionary from that land to the first Scot settlers in Alba, landing on the island of Iona in 563. After establishing Christian communities along the west coast, Columba and his brethren then turned their attention to the Picts, eventually baptizing Brude mac Maelchon, High King of the Picts in 565 and establishing the Columban Church and Christianity as the religion of the land. In 574 he crowned Aiden as King of Dalraida on the Stone of Destiny, which was possibly his own portable alter.

St. Margaret's life's work was the conversion of Scotland to Roman Catholicism from its traditional Columban Church. As wife of Malcolm Canmore she also improved trade, manufacture, the arts and improved the life of the surfs. Through such works Margaret won the love of the people. Near the end of her life, she built the austere "St. Margaret's Chapel" at Edinburgh Castle where she retreated into virtual isolation and died soon after learning of the death of Malcolm and her son. Essential differences between the Columban and Roman churches were the Columbans not recognizing the supreme authority of the Pope, celebrating Easter 40 days after lent, giving wine to parishioners at communion, and worshiping in the open air instead of in churches. Roman Catholicism became the official church of Scotland and was properly organized and consolidated under her son King David.

In these centuries, as elsewhere in medieval Europe, there were developments of the hierarchy, the parochial system and the religious houses. In this period Scotland's main links were with France, England being a common enemy. Scots were influenced by their participation in the Council of Basel in the 15th century, and the primary reforming influences in Scotland in this and the sub-sequent century were the conciliar movement, Hus, Luther, Zwingli and, above all, Calvin. The Reformation culminated in its legal establishment in 1560. In the 17th century, following the union of the Crowns of Scotland and England in 1603, attempts to con-form the Church of Scotland forcibly to the Church of England, particularly the latter's hierarchical structure and its subservience to the Crown, led to conflict and persecution, ending in 1690 with the Revolution Settlement establishing the reformed church in its Presbyterian form as the national church of Scotland.

From mid 18th to mid 19th century there was considerable controversy and schism in the church, much of it focused on the church's relations with the civil authority; the largest 'Disruption' was in 1843, when over a third of the Church seceded over freedom from civil intervention in the appointment of ministers. Since then most of those schisms have been healed, the majority of each of the separate reformed churches being now reunited, following a large reunion in 1900 and the largest in 1929. At each of the major settlements there was a minority which did not accept it: at the Reformation in 1560 some in outlying areas adhered to Rome; at the Revolution Settlement in 1690 some adhered to the Episcopalian rather than Presbyterian form; at the 1900 union some continued as The Free Church of Scotland, and at the 1929 union some continued as the United Free Church of Scotland.