Hapsburg rule brought two centuries of conflict between the Bohemian estates and the monarchy. As a result of this struggle, the Czechs lost a major portion of their native aristocracy, their particular form of religion, and even the widespread use of the Czech language. The Hapsburg policy of centralization began with its first ruler, King Ferdinand (1526-64). His efforts to eliminate the influence of the Bohemian estates were met with stubborn resistance. But the Bohemian estates were themselves divided, primarily on religious lines. By several adroit political maneuvers, Ferdinand was able to establish hereditary succession to the Bohemian crown for the Hapsburgs. The estates' inability to establish the principle of electing or even confirming a monarch made their position considerably weaker.

The conflict in Bohemia was complicated further by the Reformation and the subsequent wars of religion in Central Europe. Adherents of the Czech Reformed Church the (Hussites) opposed the Roman Catholic Hapsburgs, who were in turn supported by the Czech and German Catholics. The Lutheran Reformation of 1517 introduced an added dimension to the struggle: much of the German burgher population of Bohemia adopted the Reformed Creed (both Lutheran and Calvinist); the Hussites split, and one faction allied with the German Protestants. In 1537 Ferdinand conceded to the Czechs, recognized the Compact of Basel, and accepted moderate Utraquism. The reconciliation, however, was of brief duration.

In 1546 German Protestants united in the Schmalkaldic League to wage war against the Holy Roman Emperor, Charles V. Whereas Ferdinand wanted to aid his brother, the Hussite and pro-Protestant Czech nobility sympathized with the German Protestant princes. Armed conflict between Ferdinand and the Bohemian estates broke out in 1547. But the Bohemians were not unified; victory went to Ferdinand, and reprisals against the Czech rebels followed. The property of Czech Utraquist nobility was confiscated and their privileges abrogated. Four rebels (two lesser nobles and two burghers) were executed in the square before the royal palace. Members of the Unity of Czech Brethren, a Hussite sect that had figured prominently in the rebellion, were bitterly persecuted. Their leader, Bishop John Augusta, was sentenced to sixteen years' imprisonment. Ferdinand, now Holy Roman Emperor (1556-64), attempted to extend the influence of Catholicism in Bohemia by forming the Jesuit Academy in Prague and by bringing Jesuit missionaries into Bohemia.

Data as of August 1987