As elsewhere in Europe, the Reformation plunged the Confederation into war, with some areas staying loyal to the Pope and the old faith, and others supporting Reform.

Zurich officially adopted the Reformation in 1525, the first canton to do so. Zwingli's teaching was attractive to the urban populations of the most economically advanced cities. Apart from Solothurn and Fribourg, most of them went over to the new religion.

On the other hand he found little response among the less well educated rural population of Central Switzerland - not only for religious reasons, but because they mistrusted what they saw as over-powerful Zurich.

The cantons found it impossible to compromise. The reformed cantons made an alliance between themselves, while the Catholics, breaking the confederal oath, allied themselves to Duke Ferdinand of Austria.

Zwingli wanted to spread the new teaching throughout the Confederation, but the other Protestant cantons were not willing to join him in declaring war on the Catholics. His first attempt was thwarted by a truce in 1529, but in 1531 superior Catholic forces crushed the army of Zurich in the so-called second Kappel War and Zwingli was killed.

Under the subsequent treaty, the reformist alliance was dissolved. However, each side agreed to respect the religious choice of the other.