Borkovský later became director of the new Department of Historical Archaeology at the Institute of Archaeology; which joined the Czech Academy of Sciences in 1952.[1] He contributed greatly to the understanding of the appearance of the Prague Castle through history, particularly during the early Middle Ages. In 1950/51 he discovered the foundations of the Church of the Virgin Mary in the castle grounds which, dating from the second half of the 9th century, was the oldest church in the castle.[2] Borkovský also carried out research into the Convent of St. Agnes, Convent of St Anna and the demolished Bethlehem Chapel in the Old Town, which were important to building an understanding of the medieval development of Prague.[2] He led the investigation of the Levý Hradec until 1954 and was also involved in research into the monastery of St. Jiří.[2][1]