The shocking discovery of “thousands” of human bones and two empty graves in a Vatican cemetery has added fresh elements of mystery and intrigue to the quest to learn what happened to a papal servant’s daughter more than 35 years ago.

Emanuela Orlandi, a Vatican citizen whose father was a servant of John Paul II, vanished at the age of 15 in central Rome in 1983 in a case that has invited intrigue and conspiracy theories.

Frederica of Mecklenburg-Schwerin’s grave, like her daughter’s, was found to be entirely empty. Photo: Wikipedia

Officials searched two 19th-century graves last week at the Vatican’s Teutonic Cemetery, after an anonymous letter said to “look where the angel is pointing” – a presumed reference to an angel statue adorning the grave of Princess Sofia von Hohenlohe, who died in 1836.

However, the graves – that of Princess Sofia and Duchess Charlotte Frederica of Mecklenburg-Schwerin, who died four years later – were found to be completely empty.

In a bid to track down the remains of the noblewomen and potentially shed more light on the case, the two ossuaries were opened up.

“We did not expect to find so many bones,” Giorgio Portera, who has been hired by the Orlandi family to look into the case, said, according to Italian media.

Emanuela Orlandi’s image was a constant presence on Rome’s streets when she first went missing.

“Today, thousands are being recovered, presumably from dozens of individuals.”

Scandal might be the common link between the noblewomen’s empty coffins and the Orlandi case. Princess Charlotte was the exiled queen of Denmark, banished to Italy for an affair with her music tutor.

Now investigators are faced with yet more questions over the new remains discovered in the ossuaries. Portera spoke of “long, small and fragmented” bones and said it would take time to identify to whom they belong.

The Vatican would only confirm that remains had been found and that an “in-depth morphological examination” is to follow next Saturday.

“This activity proves once again the dedication of the Holy See to the Orlandi family,” Vatican spokesman Alessandro Gisotti said.

– with AAP