The bones were discovered this week during renovations in an annex of the Holy See's embassy in Rome.
The early speculation in the local papers was that the remains could belong to one of two young girls who disappeared 35 years ago (in separate cases): Mirella Georgi and Emanuela Orlandi.
Emanuela, who was last seen on a street in Rome, disappeared after leaving her family's Vatican City apartment to go to a music lesson in Rome. Her father was a lay employee of the Holy See.
Rome's chief prosecutor has been called in to investigate the find.
Investigators concluded that the bones belonged to a woman after examining a pelvic bone, the BBC reported. How did they make the connection?'
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Her disappearance in June 1983 was initially linked to a possible attempt by unknown persons to win freedom for Mehmet Ali Agca, the Turkish gunman who shot Pope John Paul II in 1981 and was then serving a life sentence in an Italian jail.
The Vatican statement made no mention of Orlandi. The Vatican said merely that the bones were found during work near its Rome embassy in the upscale residential neighborhood of Parioli. More recently, a leading Italian investigative journalist caused a sensation when he published a five-page document previous year that had been stolen from a locked Vatican cabinet that suggested the Holy See had been involved in Orlandi's disappearance.
The last major twist in the case came in 2012, when forensic police exhumed the body of a reputed mobster from the crypt of a Roman basilica in hopes of finding Emanuela's remains too.
The Vatican immediately branded the document a fake, though it never explained what it was doing in the Vatican cabinet. The Italian authorities are treating the matter as a homicide investigation, and the Holy See has turned the remains over to Italian authorities.