A period of rule under the Swedish House of Vasa began in the Commonwealth in the year 1587. The first two kings from this dynasty, Sigismund III (r. 1587–1632) and Władysław IV (r. 1632–1648), repeatedly attempted to intrigue for accession to the throne of Sweden, which was a constant source of distraction for the affairs of the Commonwealth. At that time, the Catholic Church embarked on an ideological counter-offensive and the Counter-Reformation claimed many converts from Polish and Lithuanian Protestant circles. In 1596, the Union of Brest split the Eastern Christians of the Commonwealth to create the Uniate Church of the Eastern Rite, but subject to the authority of the pope. The Zebrzydowski rebellion against Sigismund III unfolded in 1606–1608.

Seeking supremacy in Eastern Europe, the Commonwealth fought wars with Russia between 1605 and 1618 in the wake of Russia's Time of Troubles; the series of conflicts is referred to as the Polish–Muscovite War or the Dymitriads. The efforts resulted in expansion of the eastern territories of the Polish–Lithuanian Commonwealth, but the goal of taking over the Russian throne for the Polish ruling dynasty was not achieved. Sweden sought supremacy in the Baltic during the Polish–Swedish wars of 1617–1629, and the Ottoman Empire pressed from the south in the Battles at Cecora in 1620 and Khotyn in 1621. The agricultural expansion and serfdom policies in Polish Ukraine resulted in a series of Cossack uprisings. Allied with the Habsburg monarchy, the Commonwealth did not directly participate in the Thirty Years' War.Władysław's IV reign was mostly peaceful, with a Russian invasion in the form of the Smolensk War of 1632–1634 successfully repelled. The Orthodox Church hierarchy, banned in Poland after the Union of Brest, was re-established in 1635.