Counter-Reformation
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. They assumed judicial and financial powers over the clergy, laid down firm rules of conduct for the priests, outlawed concubinage, and reserved the right to nominate priests in the first place, who previously had been assigned by the bishoprics. They also banned printing, distributing, and possessing Reformist tracts; and banned the study of Hebrew and Greek (to put an end to the independent study of biblical sources). 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.
The Catholic cantons also maintained their domination of the Catholic Church after the Council of Trent (1545 to 1563), although they had accepted its positions. They opposed Cardinal Borromeo's plans for the creation of a new bishopric in central Switzerland. However, they did participate in the education program of Trent. In 1574, the first Jesuit school was founded in Lucerne. Others soon followed, and in 1579, a Catholic university for Swiss priests, the Collegio helvetico, was founded in Milan. In 1586, a nunciature was opened in Lucerne. The Capuchins were also called to help; a Capuchin cloister was founded in 1581 in Altdorf.
Parallel to these efforts to reform the Catholic Church, the Catholic cantons also proceeded to re-Catholicize regions that had converted to Protestantism. Besides reconversions in the common territories, the Catholic cantons in 1560 first tried to undo the Reformation in Glarus, where the Catholics were a minority.
The five Catholic cantons formed a military alliance with the Pope and the Catholic Duchy of Savoy, and had the support of Aegidius Tschudi, the Landammann (chief magistrate) of Glarus. But due to lack of money, they could not intervene in Glarus by force. In 1564, they settled for a treaty which prescribed the separation of religions in Glarus. There were henceforth two legislative assemblies (Landsgemeinde) in the canton, a Catholic and a Protestant one, and Glarus would send one Catholic and one Protestant representative each to the Tagsatzung.
The Bishop of Basel, Jakob Christoph Blarer von Wartensee, moved his seat to Porrentruy in the Jura mountains in 1529, when Basel became Protestant. In 1581, the bishopric regained the Birs river valley lying southwest of Basel. In Appenzell, where both confessions coexisted more or less peacefully, the counter-reformatory activities beginning with the arrival of the Capuchin friars resulted in a split of the canton in 1597 into the Catholic Appenzell Innerrhoden and the Protestant Ausserrhoden, which both had one vote in the Tagsatzung.
Read more about this topic: Reformation In Switzerland