stylistic:tone
Second war (1500–1503)

Hostilities were renewed in May 1500, when Ivan III took advantage of a planned Polish–Hungarian campaign against the Ottoman Empire: While preoccupied with the Ottomans, Poland and Hungary would not assist Lithuania. The pretext was the alleged religious intolerance toward the Orthodox in the Lithuanian court. Helena was forbidden by her father Ivan III to convert to Catholicism, which provided numerous opportunities for Ivan III, as the defender of all Orthodox, to interfere in Lithuanian affairs and rally Orthodox believers.

The Muscovites promptly overran Lithuanian fortresses in Bryansk, Vyazma, Dorogobuzh, Toropets, and Putivl. Local nobles, particularly the Vorotynskys, often joined the Muscovite cause. Another attack came from the southeast into Kiev Voivodeship, Volhynia, and Podolia. On July 14, 1500, the Lithuanians suffered a great defeat in the Battle of Vedrosha, and the Lithuanian Grand Hetman Konstanty Ostrogski was captured. The defeat was one of the reasons for the proposed Union of Mielnik between Poland and Lithuania. In November 1501, the Lithuanians were defeated again in the Battle of Mstislavl. The Crimean Tatars destroyed the Golden Horde, a Lithuanian ally, when its capital New Sarai was conquered in 1502.

In June 1501, John I Albert, King of Poland, died leaving his brother Alexander Jagiellon, Grand Duke of Lithuania, the strongest candidate for the Polish throne. Alexander became preoccupied with the succession. To counter religious accusations, Alexander attempted to establish a church union between Catholics and Orthodox as it was envisioned at the Council of Florence – the Orthodox would retain their traditions but would accept the pope as their spiritual sovereign. The Metropolitan of Kiev and all Rus' agreed to such an arrangement, but Helena protested. Polish nobles, including Bishop Erazm Ciołek and Cardinal Frederick Jagiellon, discussed the issue of royal divorce.

In the meantime, the war continued, just not as successfully for Moscow. As Lithuanian forces arrived in the region, the Muscovite forces had to move slowly. Additionally, the Livonian Order, led by Wolter von Plettenberg, joined the war as a Lithuanian ally. The Livonian troops won the Battle of the Siritsa River in August 1501, besieged Pskov, and won the Battle of Lake Smolino in September 1502. In 1502, Ivan III organized a campaign to capture Smolensk, but the city withstood the siege as Muscovites chose a poor strategy and had insufficient artillery. Peace negotiations began in mid-1502. Alexander asked Vladislaus II of Hungary to act as the mediator, and a six-year truce was concluded on the Feast of the Annunciation (March 25) in 1503. The Grand Duchy of Lithuania lost approximately 210,000 square kilometres (81,000 sq mi), or a third of its territory: Chernigov, Novgorod-Seversk, Starodub, and lands around the upper Oka River. Russian historian Matvei Kuzmich Liubavskii counted Lithuanian losses at 70 volosts, 22 towns, and 13 villages. The Lithuanians also acknowledged Ivan's title, sovereign of all Russia.

Historian Edvardas Gudavičius said: "The war of 1492–1494 was a kind of reconnaissance mission conducted by the united Russia. the ceasefire of 1503 showed the planned political aggression of Russia, its undoubted military superiority. The concept of the sovereign of all Russia, put forward by Ivan III, did not leave room for the existence of the Lithuanian state".

During the Muscovite–Lithuanian War of 1503, the Crimean Tatar armies pillaged the Lithuania's southern towns of Slutsk, Kletsk, and Nyasvizh and even threatened the capital city of Vilnius. Alexander Jagiellon then ordered the construction of a defensive wall around his capital, which was completed in 1522.