Forensic experts extracted bones from two ossuaries within the walls of the Vatican on Saturday as part of an investigation aimed at resolving the case of a girl who vanished in 1983.
Following an anonymous tip-off, the Vatican earlier this month opened two tombs to see if the body of Emanuela Orlandi, the daughter of a Vatican clerk, was hidden there.
Instead, they ran into a new mystery when nothing was found, not even the bones of two 19th century princesses who were supposed to be buried in the Vatican's tiny Teutonic Cemetery.
After consulting its records, the Vatican announced last week they had located bones under the floor of the Pontifical Teutonic College, which flanks the graveyard.
Structural work was carried out in the cemetery at the end of the 19th century and again about 60 years ago.
Church officials believe the remains of Princess Sophie von Hohenlohe, who died in 1836, and Princess Carlotta Federica of Mecklenburg, who died in 1840, might have been moved and never taken back to their original resting place.
The Vatican has not speculated about whose bones might have been recovered from the ossuaries on Saturday, saying only that they would now be analysed to try to establish their identities.
Amongst those present as the tiny manhole covers were removed was a representative of the Orlandi family.
Emanuela Orlandi disappeared in 1983 after she left her family's flat in the Vatican City and headed to a music lesson. She was 15 at the time.
Theories about her disappearance have run the gamut from an attempt to secure freedom for Mehmet Ali Agca, the Turk jailed in 1981 for trying to assassinate Pope John Paul II, to a connection to the grave of Enrico De Pedis, a mobster buried in a Rome basilica.
His tomb was opened in 2012 but nothing was revealed.
The Orlandi family received an anonymous letter earlier this year saying Emanuela's body might be hidden among the dead in the Teutonic Cemetery where a statue of an angel holding a book reads "Requiescat in Pace," Latin for "Rest in Peace."
The Vatican has always denied suggestions it dragged its feet over the investigation.
"With this latest expert operation ... the Vatican is once again showing its openness towards the Orlandi family. This openness has been shown from the outset in agreeing to check the Holy Teutonic Campus even on the basis of a mere anonymous report," it said in a statement on Saturday.