Inside, an altar stands behind a large wooden platform where people kneel and pray. Beneath this is a stone staircase so narrow it can admit only one person at a time. Researchers liken it to an entrance to a secret lair: The steps descend to a dark and dusty underworld.

A black metal gate leads to the labyrinthine chambers that house the corpses. Once, there were body parts piled into a pyramid on the floor and stacked on shelves that reached to the ceiling.

For most of their history, the corpses were preserved intact: Cool temperatures and ventilation in the underground chamber had caused them to undergo spontaneous mummification. (Read more about how bodies spontaneously mummify.) Though they faced disturbances over the centuries as the city and church were occupied by Napoleon, then the Nazis, it was the Soviet occupation of Lithuania that brought about a drastic change in the mummies’ fate.

In the 1960s, a forensic scientist named Juozas Albinas Markulis became one of the first to study the mummies. He wanted to know whether there were victims from World War II mixed in among the 17th-, 18th- and 19th-century corpses. (Oddly, Dr. Markulis is better known to Lithuanians not as a scientist but as a former spy who, while posing as a leader of the Lithuanian resistance, lured others into Soviet ambushes.)

Dr. Markulis and his students at Vilnius University identified 500 bodies in the crypt, of which about 200 had been mummified. In 1962, government officials inspected the crypt and ordered that the mummies be sealed behind glass, fearful that infected bodies might start an epidemic. They called it the Chamber of Death.