Human bones discovered by construction workers in the Vatican's embassy in Rome have been identified as belonging to a man who died more than fifty years ago.

The confirmation of the deceased's gender and a time frame of his death comes after much speculation that the remains could have belonged to two teenage girls who went missing in the 1980s.

The girls' disappearance has haunted Romans in the ensuing decades, reports news.com.au.

An almost complete skeleton and other bone fragments were unearthed last month during work on an annex to the Holy See's imposing embassy compound near Rome's famous Villa Borghese museum.

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In 1983 Mirella Gregori and Emanuela Orlandi went missing but authorities have been hesitant to link the two girls disappearances.

The discovery of the remains sparked media stories suggesting they might belong to Orlandi, the 15-year-old daughter of a Vatican employee who vanished in 1983, or to Gregori, who was from Rome.

Emanuela Orlandi, whose body has never been found. Photo / AP
Emanuela Orlandi, whose body has never been found. Photo / AP

The Orlandi disappearance has attracted a number of complex theories, including that she was kidnapped as part of a Cold War Soviet plan and used as a tool to blackmail Pope John Paul II; that she was involved in a sexual orgy with a Vatican based sect of Satanists or; that she was abducted by the Mafia.

Mirella Gregori's disappearance has often been linked to Orlandi's in conspiracy theories relating to Vatican financial collapses and plots to kill Pope John Paul II.

Orlandi and Gregori's bodies have never been found.

Initial reporting said the bones were believed to be female, but the local judicial source said DNA testing showed the bones were male, while carbon dating showed they predated 1964.

The disappearance of the two teenagers in 1983 attracted much attention and many theories, linking them to the Cold War and Pope John Paul II. Photo / Getty Images
The disappearance of the two teenagers in 1983 attracted much attention and many theories, linking them to the Cold War and Pope John Paul II. Photo / Getty Images

Orlandi's disappearance was initially connected 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.

In 2005, an anonymous caller to a television talk show said the secret to her kidnap was buried along with Enrico "Renatino" De Pedis, a mobster who once led the feared Magliana gang which terrorised Rome in the 1980s.

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Police eventually opened his tomb in a Rome basilica in 2012 looking for clues but came up empty-handed.

A Vatican exorcist, Gabriele Amorth, once alleged that he had discovered during his exorcism work that she had been seized by Vatican insiders and used as a sex slave.