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.
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.
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 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.
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 convert to Protestantism.
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.
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.
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, ultimately limiting Zwinglianism to parts of the Swiss confederacy and preventing its adoption in areas north of the Rhine.
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 success of the Reformation in Zürich and its rapid territorial expansion definitely made this religious renewal a political issue and a major source of conflict between the thirteen cantons.
Conflicts arose especially over the situation in the common territories, where the administration changed bi-annually among cantons and thus switched between Catholic and Protestant rules.
After numerous minor incidents and provocations from both sides, a Protestant pastor was burned on the stake in Schwyz in 1529, and in retaliation Zürich declared war.
Only strategically important places such as the Freiamt or those along the route from Schwyz to the Rhine valley at Sargans (and thus to the Alpine passes in the Grisons) were forcibly re-Catholicised.
While the official Church remained passive during the beginnings of the Reformation, the Swiss Catholic cantons took measures early on to keep the new movement at bay.
Overall, these measures were successful: not only did they prevent the spreading of the Reformation into the Catholic cantons but also they made the Church dependent on the state and generally strengthened the power of the civil authorities.
When Francesco II Sforza died in Milan in 1534, the duke's troops were bound by the French engagement there, and Bern promptly conquered the Vaud and, together with the Valais, also territories south of Lake Geneva in 1536.
The alliance of 1560 of the Catholic cantons with Savoy encouraged duke Emmanuel Philibert to raise claims on the territories his father Charles III had lost in 1536.
Geneva was thus a Protestant enclave within the Catholic territories of Savoy again and as a result intensified its relations with the Swiss confederacy and Bern and Zürich in particular.
In the night from 11 to 12 December 1602, the duke's troops unsuccessfully tried to storm the city, which definitely maintained its independence from Savoy in the peace of Saint Julien, concluded in the following summer.
Strasbourg, another Protestant city, wanted to join the confederacy in 1588, but like Geneva some twenty years earlier, it was rejected by the Catholic cantons.
The confederacy did not allow any foreign army to cross its territory: the alpine passes remained closed for Spain, just as an alliance offer of the Swedish King Gustav Adolph was rejected.
When such a feud spilled over into the Valtellina in 1619, a subject territory of the Three Leagues, the population there responded in kind, killing the Protestant rulers in 1620 and calling Habsburg Spain for help.
The mayor of Basel, Johann Rudolf Wettstein, lobbied for a formal recognition of the Swiss confederacy as an independent state in the peace of Westphalia.
With the support of Henri II d'Orléans, who was also prince of Neuchâtel and the head of the French delegation, he succeeded to get the formal exemption from the empire for all cantons and associates of the confederacy.
This solicited the response of both peasants and free citizens, who resented such curtailing of their democratic rights, and around 1523/25, also fuelled by the reformatory spirit, revolts broke out in many cantons, both rural and urban.
Contrary to the development in the Holy Roman Empire, where the hostilities escalated and the rebellion was put down by force, there were only isolated armed conflicts in the confederation.
Conrad Gessner in Zürich did studies in systematic botany, and the geographic maps and city views produced e.g. by Matthäus Merian show the beginning of a scientific cartography.
Geneva under Calvin and his successor Theodore Beza demanded their naturalisation and strict adherence to the Calvinist doctrine, whereas Basel, where the university had re-opened in 1532, became a center of intellectual freedom.