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From the beginning of the Protestant Reformation in the 1520s, Protestant doctrines were welcomed by the people living in the areas under Habsburg domination. By the middle of the sixteenth century, most inhabitants were Protestant. Lutherans predominated in German-speaking areas, except in Tirol, where the Anabaptists were influential. Nevertheless, the Roman Catholic Church retained the support of the Habsburg Dynasty and was able to maintain a strong presence throughout the area.
Religious violence and serious persecution were rare after the 1520s, and an uneasy coexistence and external tolerance prevailed for most of the sixteenth century. Ferdinand pressed Rome for concessions that would bridge the positions of moderate reformers and Catholics, but at the Council of Trent (1545-63), the Catholic Church chose instead a vigorous restatement of Catholic doctrine combined with internal reforms. The council thus hardened lines of divisions between Catholicism and Protestantism and laid the foundation for the Counter-Reformation, which the Habsburgs would pursue aggressively in the 1600s.
Source: U.S. Library of Congress