During the Protestant Reformation, the Ottoman Empire invaded Hungary (then under control of the Hapsburg Holy Roman, and Catholic, Empire). The Ottomans conquered the territory and the Hungarian people lost faith in their Catholic rulers, and in Catholicism itself, to protect them. By 1600, the vast majority of the country had converted to Protestantism, although this would be undone by the Catholic Counter-Reformation.

The ruling family of Poland remained Catholic throughout the Protestant Reformation, but the nobles and landed aristocracy were quick to embrace Protestantism. Interestingly, the peasantry generally sided with the King and with not the nobles and remained fiercely Catholic. 

The Thirty Years' War, fought from 1618 to 1648, was primarily fought as a war of religion between Protestants and Catholics. In Poland and Hungary, it contributed to the declining influence of Protestantism and the resurgence of Catholicism.

The Hussite Church emerged from the teachings of Jan Hus. Hus preached reform in the century before the beginning of the more widely impactful Protestant Reformation, but his reforming movement may be seen as part of the wider European trend. The Hussites were centered in Bohemia, in the modern day Czech Republic.

Throughout Europe, but especially in Germany, Poland, and Hungary the most important factor in determining the religious beliefs of a region or group of people was the religious beliefs of the prince or ruler of that region. If the prince embraced Lutheranism, then a large number of the people under his control would also do so.

The Protestant Reformation made rapid initial gains in both Poland and Hungary. In the century or so that followed the Protestant Reformation, the majority of both countries converted to Protestantism (either Lutheranism or Calvinism); however, both countries were overwhelmed by the Catholic Counter-Reformation, and most of the gains made by Protestants in the sixteenth century were undone in the seventeenth century.

Pogroms were organized attacks on Jewish communities in Russia carried out by the state in the nineteenth and early twentieth centuries.

During the sixteenth century, the Hungarian people were overrun by the Ottoman Empire and began to view their Catholic faith as offering inadequate protection. Subsequently, Protestantism gained rapid and almost total popularity, and by the beginning of the seventeenth century, it is estimated that over ninety percent of the population had converted away from Catholicism; however, in the seventeenth century, the Catholic Counter Reformation, led by Hungarian King Ferdinand II, fought back, and by the eighteenth century, the vast majority of Hungarians were Catholic again.

Calvinism was the most effective Protestant faith at penetrating Polish society, and it was the dominant religion in the country for several decades at the height of the Protestant Reformation; however, the Catholic Counter-Reformation was wildly successful, and Calvinism survived only in limited numbers.

The Battle of Mohacs was fought between the forces of Hungary and the Ottoman Empire in 1526. It ended in an overwhelming victory for the forces of the Ottoman Empire, which led the people of Hungary to abandon their Catholic faith, because they thought that it no longer offered the protection of God's grace. They took up Protestantism in large numbers and would hold the faith for a century or so until the Catholic Counter-Reformation returned Hungary to Catholicism.