thumb|upright=1.3|Map of the thirteen cantons of the Swiss confederacy in 1530 (green) with their separate subject territories (light green), condominiums (grey) and associates (brown)
thumb|upright=1.3|Map of the Swiss Confederacy by Sebastian Münster ()
The Protestant Reformation in Switzerland was promoted initially by Huldrych Zwingli, who gained the support of the magistrate, Mark Reust, and the population of Zürich in the 1520s. It led to significant changes in civil life and state matters in Zürich and spread to several other cantons of the Old Swiss Confederacy. Seven cantons remained Catholic, however, which led to intercantonal wars known as the Wars of Kappel. After the victory of the Catholic cantons in 1531, they proceeded to institute Counter-Reformation policies in some regions. The schism and distrust between the Catholic and the Protestant cantons defined their interior politics and paralysed any common foreign policy until well into the 18th century.
Despite their religious differences and an exclusively Catholic defence alliance of the seven cantons (Goldener Bund), no other major armed conflicts directly between the cantons occurred. Soldiers from both sides fought in the French Wars of Religion.
During the Thirty Years' War, the thirteen cantons managed to maintain their neutrality, partly because all major powers in Europe depended on Swiss mercenaries and would not let Switzerland fall into the hands of one of their rivals. The Three Leagues (Drei Bünde) of the Grisons were not yet a member of the Confederacy but were involved in the war from 1620 onward, which led to their loss of the Valtellina from 1623 to 1639.
Development of Protestantism
After the violent conflicts of the late 15th century, the Swiss cantons had had a generation of relative political stability. As part of their struggle for independence, they had already in the 15th century sought to limit the influence of the Church on their political sovereignty. Many monasteries had already come under secular supervision, and the administration of schools was in the hands of the cantons, although the teachers generally still were priests.
Nevertheless, many of the problems of the Church also existed in the Swiss Confederacy. Many a cleric, as well as the Church as a whole, enjoyed a luxurious lifestyle in stark contrast to the conditions of the large majority of the population; this luxury was financed by high church taxes and abundant sale of indulgences. Many priests were poorly educated, and spiritual Church doctrines were often disregarded. Many priests did not live in celibacy but in concubinage. The new reformatory ideas thus fell on fertile ground.
left|thumb|upright=0.8|Huldrych Zwingli (woodcut by [[Hans Asper, 1531).]]
The main proponent of the Reformation in Switzerland was Huldrych Zwingli, whose actions during the Affair of the Sausages are now considered to be the start of the Reformation in Switzerland. His own studies, in the Renaissance humanist tradition, had led him to preach against injustices and hierarchies in the Church already in 1516 while he was still a priest in Einsiedeln. When he was called to Zürich, he expanded his criticism also onto political topics and in particular condemned the mercenary business. His ideas were received favorably, especially by entrepreneurs, businessmen, and the guilds. The first disputation of Zürich of 1523 was the breakthrough: the city council decided to implement his reformatory plans and to convert to Protestantism.
thumb|upright=1.2|[[Iconoclasm in Zurich, 1524.]]
In the following two years, profound changes took place in Zürich. The Church was thoroughly secularised. Priests were relieved from celibacy and the opulent decorations in the churches were thrown out. The state assumed the administration of Church properties, financing the social works (which up to then were managed entirely by the Church), and also paid the priests. The last abbess of the Fraumünster, Katharina von Zimmern, turned over the convent including all of its rights and possessions to the city authorities on 30 November 1524. She even married the next year.
right|thumb|upright=0.8|John Calvin
Over the next few years, the cities of St. Gallen, Schaffhausen, Basel, Bienne, Mulhouse, and Bern all followed the example set by Zürich. Bern was the first to follow Zürich, in 1528, when the aftermath of the Bern Disputation officially pronounced Bern as the second Protestant Swiss canton. Their subject territories were converted to Protestantism by decree. In Basel, reformer Johannes Oecolampadius was active, in St. Gallen, the Reformation was adopted by the mayor Joachim Vadian. In Glarus, Appenzell, and in the Grisons, which all three had a more republican structure, individual communes decided for or against the Reformation. In the French-speaking parts, reformers like William Farel had been preaching the new faith under Bernese protection since the 1520s, but only in 1536, just before John Calvin arrived there, did the city of Geneva fully convert to Protestantism. The same year, Bern conquered the hitherto Savoyard Vaud and also instituted Protestantism there.
Despite their conversion to Protestantism, the citizens of Geneva were not ready to adopt Calvin's new strict Church order and banned him and Farel from the city in 1538. Three years later, following the election of a new city council, Calvin was called back. Step by step he implemented his strict program. A counter-revolt in 1555 failed, and many established families left the city.
In search of a common theology
Zwingli, who had studied in Basel at the same time as Erasmus, had arrived at a more radical renewal than Luther and his ideas differed from the latter in several points. A reconciliation attempt at the Marburg Colloquy in 1529 failed. Although the two charismatic leaders found a consensus on fourteen points, they kept differing on the last one on the Eucharist: Luther maintained that through sacramental union the bread and wine in the Lord's Supper became truly the flesh and blood of Christ, whereas Zwingli considered the bread and wine only symbols. This schism and the defeat of Zürich in the Second War of Kappel in 1531, where Zwingli was killed on the battlefield, were a serious setback, for Zwinglianism.
left|thumb|upright=0.8|Heinrich Bullinger
After Zwingli's death, Heinrich Bullinger took over his post in Zürich. Reformers in Switzerland continued for the next decades to reform the Church and to improve its acceptance by the common people. Bullinger in particular also tried bridging the differences between Zwinglianism and Calvinism. He was instrumental in establishing the Consensus Tigurinus of 1549 with John Calvin and the Confessio Helvetica posterior of 1566, which finally included all Protestant cantons and associates of the confederacy. The Confessio was also accepted in other European Protestant regions in Bohemia, Hungary, Poland, the Netherlands, and Scotland, and together with the Heidelberg Catechism of 1563, where Bullinger also played an important role, and the Canons of Dordrecht of 1619 it would become the theological foundation of Protestantism of the Calvinist strain.
The Consensus Tigurinus (Zurich Consensus) formalized the Calvinist-Bullingerian doctrine of the pneumatic presence taught in the Reformed Churches, which asserts that when communicants receive the bread and wine, they also receive the body of Christ and the blood of Christ by faith. It declared that the eucharist was not just symbolic of the meal, but they also rejected the Lutheran position that the body and blood of Christ is in union with the elements. It was this Calvinist-Bullingerian doctrine of a real spiritual presence of Christ in the Eucharist that became the doctrine of the Reformed Churches, while Zwingli's view was rejected by the Reformed Churches (though it was later adopted by other traditions, such as the Plymouth Brethren). With this rapprochement, Calvin established his role in the Swiss Reformed Churches and eventually in the wider world.,