The fact that the Confederation avoided being torn apart along religious lines during the 30 Years War, did not meant that its members had settled their differences. The confessional divide sparked two wars in less than 60 years.

These are known as the first and second Villmergen Wars, after the location in modern-day canton Aargau where the final battle was fought in each case.

The first war, in 1656, was the result of an attempt by Zurich to improve the situation of Protestants in Catholic-ruled areas, but ended in defeat for the Protestants.

The second war, in 1712, was sparked by a dispute between the Reformist population of Toggenburg and the Catholic St Gallen monastery over the construction of a road linking the central cantons with southern Germany. Zurich and Bern supported the Toggenburgers and defeated the Catholic side.

The subsequent peace treaty substantially altered the balance of power between the Catholic and Reformed cantons. The Catholics were no longer dominant.