During the Renaissance and the Protestant Reformation an independent Dutch religious tradition began to take shape in the northern parts of the independent Netherlands. The most prominent Dutch theologian was the humanist Desiderius Erasmus. Erasmus worked in the midst of the growing Reformation. He was critical of the abuses within the Catholic Church and called for reform, but he kept his distance from Luther and Melancthon. He continued to recognise the authority of the pope. Erasmus emphasized a middle way, with a deep respect for traditional faith, piety and grace, and rejected Luther's emphasis on faith alone. Erasmus therefore remained a Catholic all his life. In relation to clerical abuses in the Church, Erasmus remained committed to reforming the Church from within. He also held to Catholic doctrines such as that of free will, which some Reformers rejected in favour of the doctrine of predestination. His middle road approach disappointed and even angered scholars in both camps.
The 16th and 17th century were characterized by the Protestant Reformation, which greatly influenced the history of the Netherlands, especially in western and northern areas of the country. The first wave of Reformation, initiated by Martin Luther, did not come to the Netherlands. The second wave of the Protestant Reformation, Anabaptism, became very popular in the counties of Holland and Friesland. Anabaptists were very radical and believed that the apocalypse was very near. They refused to live the old way, and began new communities, creating considerable chaos. A prominent Dutch anabaptist was Menno Simons, who initiated the Mennonite church. Another Anabaptist, Jantje van Leyden became the ruler of a newly founded city, New Jerusalem. Anabaptists survived throughout the centuries and they were recognized by the States-General of the Netherlands in 1578. Institutionalized Dutch baptism stood for a model for both English and American Baptists. The third wave of the Reformation, Calvinism, arrived in the Netherlands in the 1540s, converting both parts of the elite and the common population, mostly in Flanders. The Spanish government, under Philip II started harsh persecution campaigns, supported by the Inquisition. In reaction to this persecution, the Calvinists rebelled. First there was the Beeldenstorm in 1566, which involved the destruction of religious depictions in churches. Also in 1566 William the Silent, a convert to Calvinism, started the Eighty Years' War to liberate the Calvinist Dutch from the Catholic Spaniards. The counties of Holland and Zeeland were conquered by Calvinists in 1572. A considerable number of people were Calvinist in Holland and Zeeland at that time already, while the other states remained almost entirely Catholic. The estates of Holland, led by Paulus Buys decided to support William the Silent, the Prince of Orange. All churches in the Calvinist territories became Calvinist and most of the population in these territories converted to or were forced to convert to Calvinism. Because the Netherlands had ceded from Spain over both political and religious issues, it practiced certain forms of tolerance towards people of certain other religions and opened its borders for religious dissenters (Protestants and Jews) from elsewhere, while maintaining its persecution and later discrimination against native Catholics. Descartes for instance lived in the Netherlands for most of his adult life.
In the early 17th century the Roman Catholic Jesuits launched large campaigns in order to rekindle faith among Catholics. Many Catholics were tending towards converting to Protestantism for temporal gain, and in those areas where the Jesuits could operate, the Dutch Catholics were supported in their faith and some Calvinists reverted to Catholicism. The number of adherents of Catholicism however dwindled due to the lack of priests, especially in rural areas of Gelre, Overijssel, Groningen and Frisia. At the same time, the larger western cities received an influx of Protestant immigrants from Germany, Flanders and France and developed a Protestant character. Orthodox Calvinists converted a belt of land from the south west (the province of Zeeland), via the Veluwe, to the north of the Netherlands (until the city of Staphorst) during the 17th and even as late as the 18th centuries. This remains Orthodox Calvinist until this day. During the Twelve Years' Truce (between 1609 and 1621) in the Eighty Years' War, the Netherlands saw a civil war along religious lines. The Synod of Dort tried to bring an end to an internal theological conflict within the Calvinist church between two tendencies of Calvinism the orthodox Gomarists or Contra-Remonstrants and the liberal Arminians or Remonstrants. Civil war broke out in the 1610s between orthodox and liberal Calvinists. The liberal sovereign estates of Holland left the Republic. The orthodox Calvinist side won (prince Maurice of Orange and the other provinces) and the official head of state of the County of Holland, Johan van Oldebarnevelt, was executed. Calvinism became the de facto state religion and political offices could only be occupied by Calvinists (and in some cases, Jews). Other Christian religions were mostly tolerated, although discriminated, but were not permitted to practice their religion in public. Judaism was allowed in public, Lutheranism only in larger cities on the condition of maintaining Calvinist church interior styles, without crucifixes as known in Scandinavian cathedrals. In 1648, the independence of the Netherlands was recognized by the Treaty of Westphalia. The Netherlands did not only include the seven relatively independent Protestant provinces of the Dutch Republic but also a Roman Catholic Generaliteitsland, which was governed by the States-General. This area roughly includes the current provinces of North Brabant and Limburg, which remained Roman Catholic. The Netherlands became known among Anglicans, many Protestants and Jews for its relative religious tolerance and became a refuge for the persecuted and a home for many of these migrants. The proportion of first-generation immigrants from outside the Netherlands among the population of Amsterdam was nearly 50% in the 17th and 18th centuries.[citation needed] Jews had their own laws and formed a separate society. Many Jews, especially from Antwerp, migrated to Amsterdam. The Netherlands also hosted religious refugees, including Huguenots from France and Puritans from England (the most famous of the latter being the Pilgrims).
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