In 1278, Henry, the abbot of the Cistercian monastery in Sedlec, was sent to the Holy Land by King Otakar II of Bohemia. He returned with him a small amount of earth he had removed from Golgotha and sprinkled it over the abbey cemetery. The word of this pious act soon spread and the cemetery in Sedlec became a desirable burial site throughout Central Europe.
In the mid 14th century, during the Black Death, and after the Hussite Wars in the early 15th century, many thousands were buried in the abbey cemetery, so it had to be greatly enlarged.
Around 1400, a Gothic church was built in the center of the cemetery with a vaulted upper level and a lower chapel to be used as anossuary for the mass graves unearthed during construction, or simply slated for demolition to make room for new burials.
After 1511, the task of exhuming skeletons and stacking their bones in the chapel was given to a half-blind monk of the order.
Between 1703 and 1710, a new entrance was constructed to support the front wall, which was leaning outward, and the upper chapel was rebuilt. This work, in the Czech Baroque style, was designed by Jan Santini Aichel.
In 1870, František Rint, a woodcarver, was employed by the Schwarzenberg family to put the bone heaps into order, yielding a macabre result.