In the 16th century, Protestant Reformation movements made deep inroads into Polish Christianity and the resulting Reformation in Poland involved a number of different denominations. The policies of religious tolerance that developed in Poland were nearly unique in Europe at that time and many who fled regions torn by religious strife found refuge in Poland. The reigns of King Sigismund I the Old (1506–1548) and King Sigismund II Augustus (1548–1572) witnessed an intense cultivation of culture and science (a Golden Age of the Renaissance in Poland), of which the astronomer Nicolaus Copernicus (1473–1543) is the best known representative. Jan Kochanowski (1530–1584) was a poet and the premier artistic personality of the period. In 1525, during the reign of Sigismund I, the Teutonic Order was secularized and Duke Albert performed an act of homage before the Polish king (the Prussian Homage) for his fief, the Duchy of Prussia. Mazovia was finally fully incorporated into the Polish Crown in 1529.

The reign of Sigismund II ended the Jagiellonian period, but gave rise to the Union of Lublin (1569), an ultimate fulfillment of the union with Lithuania. This agreement transferred Ukraine from the Grand Duchy of Lithuania to Poland and transformed the Polish–Lithuanian polity into a real union, preserving it beyond the death of the childless Sigismund II, whose active involvement made the completion of this process possible.

Livonia in the far northeast was incorporated by Poland in 1561 and Poland entered the Livonian War against the Tsardom of Russia. The executionist movement, which attempted to check the progressing domination of the state by the magnate families of Poland and Lithuania, peaked at the Sejm in Piotrków in 1562–63. On the religious front, the Polish Brethren split from the Calvinists, and the Protestant Brest Bible was published in 1563. The Jesuits, who arrived in 1564, were destined to make a major impact on Poland's history.