7 September 1993 Pope St. John Paul II visited Šiluva. The Holy Father prayed in the Chapel of the Apparition of the Blessed Virgin Mary and took part in the Liturgy of the Word in the Basilica of the Nativity of the Blessed Virgin Mary.

The Pope, as if echoing the message that the Virgin Mary conveyed to the shepherd children during the apparition, said that Mary directed her whole life toward Christ. She invites us to do the same: “Do whatever He tells you” (Jn 2:5). “In Cana, you asked your Son to turn water into wine. Help the Lithuanian nation to transform the painful experience of the past into a joyful future,” the Holy Father prayed in Šiluva.

2003 after restoration, the miraculous image of the Blessed Virgin Mary with the Child was returned to the high altar of the Šiluva Basilica; in 2006, it was crowned with crowns blessed by Pope Benedict XVI.

2003during the Šilinės indulgence feast, marking the tenth anniversary of the Holy Father’s visit, Archbishop Sigitas Tamkevičius SJ blessed the John Paul II House, which today serves the spiritual formation of priests and other faithful, hosts retreats and seminars for various Lithuanian communities and individuals, and accommodates pilgrims.

2008 during the celebration in Šiluva of the 400th anniversary of the apparition of the Blessed Virgin Mary, a monument to Pope John Paul II was unveiled in the sacred square to commemorate the 15th anniversary of his visit to Lithuania (sculptor: Prof. Czesław Dźwigaj of the Kraków Academy of Fine Arts); at the same time, the street next to the square was named after the Pope.

2007 the parish of Šiluva marked the 550th anniversary of its establishment.

6–15 September 2008 during the solemn celebration of the 400th anniversary of the apparition of the Blessed Virgin Mary, Šiluva was visited by the envoy of the Holy Father Benedict XVI, Cardinal Joachim Meisner, Archbishop of Cologne.

During the ten days of the Jubilee, up to 150,000 pilgrims visited Šiluva—not only from Lithuania, but also from nearby and more distant countries of Europe and America, from Australia, and individually from Asia and Africa. It was precisely at that time that the name of Šiluva spread widely throughout the world: news agencies reported on the apparition of Mary and the shrine of Šiluva. For the first time in the history of Šiluva—once marked by confessional tensions—ecumenical services were held, attended by representatives of several Christian Churches and communities.

In preparation for the Jubilee, through the care and initiative of Kaunas Archbishop S. Tamkevičius, and with the support of the Kaunas Archdiocese community, various sponsors, and donors, a pre-war plan was realized to connect the Šiluva Basilica with the Chapel of the Apparition by creating a sacred space.

In the renovated square, in addition to the already mentioned memorial to St. John Paul II, a restored statue of the Blessed Virgin Mary was erected—a precise bronze replica of the earlier one. A Pilgrim Information Centre was built, and the Šiluva History Museum was opened within it. On both sides of the square, artistic roadside shrines of the Rosary were installed for prayer. The Basilica and the Chapel of the Apparition have been gradually restored, and the white 44-meter-high tower of the chapel continues to greet pilgrims approaching Šiluva even today from afar.

2009 by decree of Kaunas Archbishop S. Tamkevičius, Days of the Sick are held in Šiluva on the last Friday of each month.

9 April 2009 by decree of the Metropolitan Archbishop of Kaunas, Sigitas Tamkevičius, in response to the sincere devotion of the faithful and with the aim of more widely spreading the message of the apparition of the Blessed Virgin Mary in Šiluva, the Society of the Blessed Virgin Mary of Šiluva was established.

2011 The Šilinės indulgence feast began to be celebrated from 7 September (previously it had started on 8 September) and continues, as usual, until 15 September. From then on, the first day of Šilinės has always been dedicated to Pope St. John Paul II, who visited Šiluva on 7 September 1993.

2013 A Pilgrim Path with 14 Stations of the Cross was also established and blessed on 25 August. It is a route of approximately 2 km through the Šiluva pine forest, leading to the Chapel of the Apparition.

2016 on the occasion of the Extraordinary Jubilee of Mercy, the Holy Doors of Mercy were opened in the Šiluva Basilica.