According to legend, the sanctuary of the martyrdom of St Stanislaus, as recognisable as Wawel Castle or St Mary's Basilica, has for almost a thousand years been a place of pilgrimage of the faithful devoted to the cult of St Stanislaus, and for over a century, a site of homage to the laity (the National Pantheon).

The first Romanesque Church of St Michael the Archangel stood here on the site of a pagan cult as early as the 11th century. Here, in 1079, Bishop Stanislaw of Szczepanów was murdered on the orders of King Boleslaw the Bold. According to the legend recorded as early as the 12th century, his dismembered remains were miraculously rejoined and his body was made whole, and the bishop was then moved to Wawel Castle. In the 13th century, Bishop Stanislaus was declared a saint and recognised as the patron saint of Poland. In the 14th century, Casimir III the Great erected a new Gothic temple. Since 1472, it has been looked after by the Pauline Order brought to Kraków by Jan Długosz. The church, destroyed during the Swedish invasion, was razed to its foundations, and in its place a Baroque church designed by Anton Munzer and modified by Antonio Solari was erected between 1733 and 1751. The main altar of the church contains a painting of the Archangel Michael from 1758, the work of Tadeusz Kuntze. The altar of St Stanislaus includes a relic of his and an image of the saint from the 17th century. Close to the church is a pond of St Stanislaus called the Polish Stoup, a likely site of pagan rituals. As legend has it, the body of the murdered Stanislaus was unceremoniously dumped next to the pond. An 18th-century statue of the bishops stands in the middle of the pond, which itself is enclosed within a 17th-century baroque stone wall. On the 750th anniversary of the canonisation of Bishop Stanislaus (1253), Pope John Paul II elevated the church to the rank of basilica minor.

The most important feast of national significance at the sanctuary is 8 May, the day of the procession with the relics of St Stanislaus from Wawel to Skałka, drawing crowds of the faithful and attendance by the highest dignitaries of Church and State. The cult of Bishop Stanislaus, a saint and martyr of the Catholic Church, began when his relics were transferred to Wawel Castle. It was from him that the legend of Poland's division as punishment for the sacrilegious murder of a servant of God grew, proclaiming that Poland disintegrated like the limbs of a quartered bishop. It was also believed that, through the intercession of Bishop Stanislaus, just as his body was reunited after his death, Poland would also overcome the division it had been subjected to, and would unite. Bishop Stanislaus was hailed as the patron saint of unification, and almost all Polish kings, beginning with Ladislaus I, were crowned kneeling before the sarcophagus of St Stanislaus in Wawel Cathedral.

The basilica is also a national pantheon. Many distinguished Poles are buried in the Crypt of Merit beneath the church, designed by Teofil Żebrawski. The remains of Jan Długosz, who was buried in Wawel Cathedral in 1480, were transferred to Skałka in 1792 and placed in a sarcophagus in the crypt in 1880. Also, at eternal rest here are the painter and playwright Stanisław Wyspiański, the poet Czesław Miłosz, the painter Jacek Malczewski and the musician and composer Karol Szymanowski.