(David Madison/Getty Images)

Italian police are poring over bones found in 200 boxes in a mobster's crypt, searching for clues to what happened to a 15-year-old girl who disappeared nearly 30 years ago, an unsolved mystery that has haunted Italians ever since.

Italian police forensic experts and coroners Monday swarmed in and around the crypt in the Basilica di Sant' Apolinare in the historic center of Rome, a few steps away from the famous Piazza Navona square where tourists like to linger. They were exhuming the coffin of a renowned Roman crime clan boss, Enrico De Pedis, who was shot to death in a market square in the center of the city in 1990, in search of bones or clues in the disappearance of 15-year old Emanuela Orlandi.

Orlandi, the daughter of a Vatican bank employee who lived with her family inside Vatican city, just across the river from the Basilica, disappeared in 1983, on her way to an afternoon music lesson that was held in a building close to the Basilica.

Since then her family has been determined to find her and has made repeated appeals to the press for help and information.

Numerous conspiracy theories have been built around Orlandi's disappearance, fueled by rumors and reports of mysterious sightings of her living in various foreign countries.

One such theory was based on the belief that Orlandi's remains would be found in this Roman crypt where the notorious mobster was buried. The belief was started when leaked reports stated that the mobster's girlfriend had allegedly accused him of killing the teen. Anonymous calls to the press over the years have called on inspectors to look inside De Pedis' coffin to see whose body was inside.

With renewed vigor, investigators have resumed their search for clues to Orlandi's disappearance and are determined to ascertain all possible leads have been followed and checked. Giuseepe Pignatore, the city's chief prosecutor said this latest search was just part of the ongoing investigation into the girl's disappearance.

The investigators worked fast, and with the help of a make-shift lab set up in the courtyard of the church, were able to quickly identify that it was indeed the Magliana clan boss De Pedis' body in the coffin in the church's crypt.  His body was in relatively good condition, dressed in a dark suit and black tie and there was no trace of anyone else in the coffin, police said.

But investigators also found about 200 boxes of unidentified bones in the crypt, which they are now working on dating. Investigators spent today checking the walls behind the boxes where the bones were kept, in case it hid secret vaults.

Vittorio Rizzo, head of the Rome crime squad told Italian TV today that the old bones found in the crypt all seem to date from pre-Napoleonic times, but it will take forensic experts a number of days to establish this. He said any more recent bones found would be taken away for DNA testing.

Since Orlandi's disappearance, the theories about what happened to her have been entwined with numerous murky stories involving the Vatican - like the attempted assassination attempt on Pope John Paul II and his would-be assassin, Ali Agca - along with a variety of other unsolved mysteries that allegedly link the church with shady financial dealings and organized crime.

Vatican spokesman Father Federico Lombardi told reporters the Vatican had no objection to the opening of the tomb.

"All possible steps must be taken to reach a conclusion in the investigation," he said, and he called the inspection of the crypt "a positive move."

De Pedis' body, which just a few years after his death, rather mysteriously and discreetly ended up buried next to a cardinal's tomb in this historic and prestigious church, will now be transferred to a public cemetery. The Vatican has said this will be done in "agreement with his family members."

Orlandi's family, who have been stubbornly insistent that the search must continue, said they are eager to hear what investigators have found in the crypt.

"Yesterday was an important day, at least to remove any doubts we had," Orlandi's brother, Pietro Orlandi, said today. "It was right that an inspection was carried out so as to follow all leads. I never believed Emanuela could be there and I don't believe it now. If more recent bones are found, they will be analyzed, but only to remove our doubt."

He said he was pleased that the Vatican was willing to help and support the investigation.

"One thing is certain: there is a link between Pope John Paul II's assassination attempt, the death of Calvi [Italian banker dubbed 'God's banker' who was found hanging in 1982 from Blackfriars Bridge in London, another murky Vatican mystery] and the disappearance of Emanuela," he said. "There has never been any proof of Emanuela's death, so we have to continue to search for her alive. Over these last 29 years, this is the first lead that has been fully followed, so we are glad whatever the results."

All the family have been stubbornly insistent that the search must continue. Her family hope that if no trace of Orlandi is found in the crypt they can keep on searching and hoping to find her alive. Her brother has said he plans to lead a march to the Vatican later this month in the hope that he can get the pope to mention his sister in a public statement.

The Vatican also hopes that this latest church search will dispel all theories of Vatican involvement, and Lombardi reiterated that the prosecutors investigating this case could "continue to count on the full support of the church authorities."

Prosecutors have said that the investigation will probably be formally closed by the Fall. So far five people are suspected of being involved in Orlandi's death, all linked to De Pedis' vicious clan, which was active in Rome in the 1970s and '80s.

At the close of the investigation the prosecutors will have to determine whether to formally accuse them or drop the case.