Senieji Gardai, where the Calvaries were brought from Western Europe in the first half of the 17th century, for the first time is mentioned in written sources in 1253. The first church in this part of Samogitia was built in 1593. Later, in 1619, another little church, the church of St. John the Baptist was erected on the St. John Hill, and a parish established in 1622. Samogitian bishop Jurgis Tiškevičius invited the Dominicans to Gardai in 1637, donating land to them and building houses for them. On the instruction of Jurgis Tiškevičius the Dominicans founded here the Kalvarijos Kalnai (Calvary Hills). Little chapels were built (in 1639) and the Dominican monks wrote hymns, prayers, and established the ways for practicing in this especially popular practice of piety in the Catholic Church. From the Calvaries which were established at Gardai, the place became to be known as the Žemaičių Kalvarija (Samogitian Calvary). In Žemaičių Kalvarija the Dominican type of calvary – 20 stations – were established, these Calvaries are among the first ones in the Grand Duchy of Lithuania (together with Vilnius – Verkiai in 1665).
From the middle of the 17th century the Žemaičių Kalvarija became famous for its miraculous painting of the Blessed Virgin Mary with Infant, and the famous Atlaidai (religious feast) of the Holy Mother Mary Visitation. The miraculous painting of the Blessed Virgin Mary, brought from Rome to the Žemaičių Kalvarija by the Dominican Petras Pugačevskis, is famous for miracles from its very placement in the side altar of the church. From 1643 this painting is considered to be miraculous. The miracles were recorded in a book, which, unfortunately, was destroyed during the church fire in 1896. The miraculous powers of the painting are also witnessed by the votum (Lat. - donation as a sign for a vow, promise to God), of which at this time there are over 150 in the Basilica. Prayers and psalms dedicated to the Žemaičių Kalvarija Mother of God were printed in 1681 in the prayer book Rožančius (The Rosary) written and issued by Jurgis Kasakauskis. These psalms The Gracious Queen and Holiest Mother Of The Divine Lord are chanted up to this day.
The bishop A. Tiškevičius conferred the title of the Holy Mother Mary Visitation for the church then being built in Kalvarija. The Visitation Atlaidai were joined to the Calvary Hills Atlaidai celebrated already earlier and gaining increasing popularity. The Atlaidai of the Žemaičių Kalvarija Holy Mother Mary Visitation begins on July 2 and lasts for as long as ten days. Since 1649 Žemaičių Kalvarija church enshrines the relics of the Holy Cross, brought from the Dominican monastery in Lublin. It is 3.2 cm long and 0.6 cm wide – the largest in the Baltics.
The Dominicans administered at Žemaičių Kalvarija until 1889 when the tsarist authorities expelled them. From 1927 until 1948 the shrine and parish of Žemaičių Kalvarija was in the custody of the Marian monks. During the years of the Soviet occupation (1940–41, 1944–89), despite huge efforts of the atheistic authorities to destroy the Calvaries, the chapels and live tradition of Hills’ visitation were upheld by people. At the request of Antanas Vaičius, Telšiai bishop at that time, in 1988 the Pope John Paul II vested the Basilica title to Žemaičių Kalvarija’s The Holy Mother Mary Visitation Church. The original name of Žemaičių Kalvarija, that had been renamed to Varduva by the Soviet authorities in 1967, was returned to this small town in1989.
On June 23, 2006 the Pope Benedict XVI consecrated the papal crowns for the Žemaičių Kalvarija’s painting of Blessed Virgin Mary with Infant, and obligated to dignify this painting the title of The Queen of Christian Families. The coronation festivity day is 8th of October 2006.
On the second day of every month, monthly Atlaidai of the Holy Mother Mary Visitation are held in the Basilica. On every Saturday believers visit the Basilica and honour the Holy Lady. For many ages Žemaičių Kalvarija was one of the major spiritual centres not only of Samogitia but of the entire Lithuania, and remains as such in the 21st century as well.