The capitulary and parish church was established by prince Vratislav II in the 2nd half of the 11th century according to the model of the Roman Church of St. Peter and Paul, when the prince began to build his seat at Vyšehrad as a purposeful opposite to Prague Castle. According to a legend, Vratislav supposedly brought 12 baskets of stones for the building’s foundations. That is also related to the founding of the canonry, which was independent on the Prague archbishop and subordinated directly to the pope in Rome. This independence was only abolished in 1763.The last reconstruction, which gave the church its present appearance, was completed in 1903. It has passed through many building eras over 900 years of its existence. From the original Romanic basilica in the 11th century, past the high-Gothic appearance in the time of Charles IV, when a three-aisle church was built with side chapels, Baroque reconstruction in the 1720s according to a project of Giovanni Santini managed by František Maxmilián Kaňka, and new-Gothic reconstruction initiated in 1885 by architect Josef Mocker. High front pseudo-Gothic towers in the front were built in 1902 - 3 according to a design of František Mikš, and at this time, Baroque bellfry from 1678 was removed.
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