Reflecting upon the course of the Reformation in 1557, Heinrich Bullinger, successor to Zwingli and leader of the reformed church in Switzerland from 1532 until 1575, presented a gloomy and pessimistic assessment. God had revealed his truth to the German nation in these times and his people had proved themselves ungrateful. The immediate consequence of this infidelity, Bullinger believed, were the dreadful wars between the Emperor and the Protestants ravaging Europe. France, Germany and Italy were engulfed in battles, and Swiss soldiers, despite the persistent opposition of the reform movement to mercenary service, continued to die on foreign territory. Within the Confederation the Protestant cities of Basle and Berne pursued their protracted quarrels with Calvin's Geneva over matters of doctrine and church polity, whilst the Catholics, strengthened by the Council of Trent, were everywhere resurgent.

The despair of the aging reformer at his desk in Zurich accurately reflects the general disappointment among Swiss reformers that the soaring hopes of the first generation had not been fulfilled. The Reformation had not, as Zwingli had originally anticipated, culminated in a unified alliance of evangelical states under the leadership of Zurich. Instead half the Confederation remained defiantly loyal to Catholicism, and even those states which had eventually followed Zurich into the Protestant camp pursued their own models of reform with a stubborn and, at times, cantankerous independence. Any survey of the Reformation in Switzerland should reflect this enduring diversity, a phenomenon which has to some extent been masked by the subsequent success of Zurich and Geneva in impressing their reforming ideals on a wider European movement later in the century.