Apart altogether from the question of religion, there was a natural opposition between populous and manufacturing centres like Berne and Basle, and the rural cantons, devoted almost entirely to agricultural and pastoral pursuits. When religious differences supervened to accentuate the rivalry already in existence, they led almost inevitably to the division of Switzerland into two hostile camps.
Zurich, Basle, Berne, Schaffhausen, and St. Gall, though they were the most important cities, soon found themselves unable to force their views on the rest of the country, as they were withstood by the federal council, the majority of which was still Catholic. The latter insisted that a conference should be held to settle the religious disputes. The conference was arranged to take place at Baden in 1526.
Eck, assisted by two other Catholic theologians, Faber and Murner, undertook to defend the Catholic position. Zurich refused to send representatives, but the reforming party were represented by Oecolampadius, Haller, and others of their leaders. The conference was attended by delegates from twelve cantons, and was approved of by the Swiss bishops. After a discussion lasting fifteen days during which Eck defended the Catholic doctrine regarding the Mass, Eucharist, Purgatory, and the Intercession of the Saints, the majority of the cantons decided in his favour, and a resolution was passed forbidding religious changes in Switzerland and prohibiting the sale of the works of Luther and Zwingli.
It was soon evident, however, that peace could not be secured by such measures. The rural and Catholic cantons were in the majority, much to the disgust of flourishing cities like Berne and Zurich. These states, believing that they were entitled to a controlling voice in the federal council, determined to use the religious question to bring about a complete change in the constitution of the country by assigning the cantonal representation in the federal council on the basis of population. They formed an alliance with the other Protestant cantons and with Constance to forward their claims (1527-8), but the Catholic cantons imitated their example by organising a Catholic federation to which the Archduke, Ferdinand of Austria, promised his support (1529).
Zwingli was most eager for war, and at his instigation the army of Zurich, backed by Berne, took the field in 1529. The Catholic states, however, made it clear that they were both able and willing to defend the constitution, but the bond of national unity and the dislike of civil war exercised such an influence on both parties that a conflict was averted by the conclusion of the Peace of Kappel (1529). The concessions secured for his party by this Peace did not satisfy Zwingli, who desired nothing less than the complete subjugation of the Catholic cantons. Negotiations were opened up with Philip of Hesse, with the German Lutherans, and with Francis I. of France, and when the news of the formation of the League of Schmalkald reached the Protestants of Switzerland, it was thought that the time had come when the triumph of Zurich and Berne, which meant also the triumph of the new teaching, should be secured. Zwingli besought his followers to issue a declaration of war, but it was suggested that the reduction of the Catholic cantons could be secured just as effectively by a blockade. In this movement Zurich took the lead. The result, however, did not coincide with the anticipations of Zwingli. The Catholic cantons flew to arms at once, and as their territories formed a compact unit, they were able to put their united army into the field before the forces of Zurich and Berne could effect a junction. The decisive battle took place at Kappel in October 1531, when the Zwinglians suffered a complete defeat, Zwingli himself and five hundred of the best men of Zurich being left dead on the field. The army of Berne advanced too late to save their allies or to change the result of the war. The Catholic cantons used their victory with great moderation. Instead of crushing their opponents, as they might have done, they concluded with them the second Peace of Kappel (1531).
According to the terms of this treaty, no canton was to force another to change its religion, and liberty of worship was guaranteed in the cantonal domains. Several of the districts that had been wavering returned to the Catholic faith, and the abbot of St. Gall was restored to the abbey from which he had been expelled.
Oecolampadius followed Zwingli to the grave in a short time, having been carried off by a fever about a month after the defeat of Kappel, and the leadership of the movement devolved upon their successors, Bullinger and Myconius.
With regard to the Sacraments Luther and Zwingli agreed that they were only signs of grace, though in the explanation of this view Zwingli was much more extreme, because much more logical, than Luther.