The conflicts between rulers and subjects in Lucerne, Bern, Solothurn and Basel culminated in 1653 in the Swiss Peasants’ War. The religiously motivated Villmergen Wars of 1656 and 1702 led to the loss of Catholic supremacy.

Peasant uprisings

The Thirty Years' War also saw repeated rebellions by peasants who were protesting against the high taxes which were collected by the city cantons.
Finally, the conflict came to a head when the authorities in Bern and Lucerne devalued their currencies in February 1653. The resentment on the part of the Bernese and Lucerne peasants also spread to the cantons of Solothurn and Basel. The peasant uprising was soon crushed, and by the end of June the authorities had retaken control of the cantons.
Ultimately all the rebels were defeated. The leaders were punished with fines, exile or death. Despite its bloody suppression, the Peasants’ War had a lasting impact. By 1798, the authorities no longer dared to levy direct taxes on the peasants. This resulted in the cities lacking the financial resources to extend their planned standing armies and bureaucracies. The thrifty Swiss militia system, administratively and militarily – in some cases up to the 20th century – is a consequence of the Peasants' War.

The Villmergen Wars

In Switzerland, since the Reformation there had been a gap between the reformed, more centralised and progressive urban areas and the Catholic, rather particularistic and conservative rural areas. After the Catholic areas emerged victorious in the Second Kappel War, the Second Kappel Peace enabled them to add political supremacy within the Confederation to their territorial gains.
That the Confederates were able to agree not to intervene in the Thirty Years' War did not mean that they had solved their religious conflicts. On the contrary: Within 60 years there another two religious wars. As these decisive battles were both waged in Villmergen (now part of Canton Aargau), they are known as the First and Second Villmergen War respectively.
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 monastery of St. Gallen over the construction of a road linking the central (Catholic) cantons with (Catholic) southern Germany. Bern and Zurich supported the Toggenburgers and defeated the Catholic side.
The subsequent peace treaty altered the balance of power between the Catholic and Reformed cantons. The Catholics were no longer dominant. The so-called Peace of Aarau of 11 August 1712, the fourth Peace in the history of the Confederation, gave Bern and Zurich supremacy in the common lordships (areas that were conquered by more than one of the ruling Old Places and commonly managed as bailiwicks). Thus, since 1531 the existing political hegemony of the Catholic Places in the common lordships was terminated. At the same time, this also meant the restoration of a balanced religious peace in the Old Confederacy.

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