Rome (CNN) -- The body of a mobster buried among cardinals and bishops on a Vatican property has been exhumed in an investigation into a teenage girl's disappearance.
Investigators at the church of Sant'Apollinare in central Rome opened the tomb of Enrico "Renatino" De Pedis on Monday in the search for clues about what happened to Emanuela Orlandi, the daughter of a prominent Vatican employee.
The 15-year-old vanished without a trace after leaving her Vatican apartment for music lessons on the afternoon of June 22, 1983.
The mystery has captivated people throughout Italy and triggered numerous conspiracy theories.
In the crypt, in addition to De Pedis' body, investigators found dozens of boxes of human bones, which they are testing.
At the time of Emanuela's disappearance nearly 30 years ago, a witness reported seeing a girl who fit her description getting into a dark green BMW near the music school, which was adjacent to the Sant'Apollinare church.
That lead was never corroborated.
In 1981, two years before the girl's disappearance, Turkish national Mehmet Ali Agca shot Pope John Paul II.
In the days after Emanuela disappeared, her parents received anonymous phone calls from someone promising the safe return of their daughter if the Vatican released Agca.
Meanwhile, an anonymous caller told police that Emanuela was kidnapped to keep her father, Ercole Orlandi, quiet.
That caller said Ercole Orlandi had stumbled upon sensitive documents that tied banker Roberto Calvi to an organized crime syndicate. Calvi was known as "God's banker" for his close association with both the Holy See and its primary banking facility, Banco Ambrosiano.
Orlandi worked in the Vatican's special events office that organizes papal functions and Catholic celebrations.
Calvi was found hanged in London in 1982. Speculation turned from suicide to homicide in that case. The tipster to police in Italy said Orlandi's daughter was nabbed to ensure her father's silence.
Ercole Orlandi died in 2004.
In 2005, another anonymous call to an Italian detective said Emanuela was kidnapped on the orders of the then-vicar of Rome, Cardinal Ugo Poletti, and that "the secret to the mystery lies in a tomb in Sant'Apollinare basilica" -- specifically De Pedis' tomb.
De Pedis was gunned down in Rome in 1990 and his body was moved to the basilica some time before 1997, presumably either as part of a secret deal for a massive loan De Pedis made to the Vatican or to protect his tomb from being desecrated by rival gang members.
In 2008, De Pedis' mistress said he was involved in Emanuela's kidnapping and that the girl was buried under the foundation of a house outside of Rome. Investigators searched that house but found that the concrete foundation was poured the year before the girl's disappearance and could not have been connected to the crime.
The Vatican has distanced itself from the Orlandi controversy.
In a three-page letter broadcast on RAI television, Vatican spokesman Federico Lombardi said he asked Vatican cardinals whether the Vatican's failure to collaborate in the original kidnapping probe was "normal and justifiable affirmation of Vatican sovereignty, or if in fact circumstances were withheld that might have helped clear something up."
The Vatican cooperated immediately with the exhumation.
After opening the tomb Monday, investigators found De Pedis' body so well preserved that scientific police were able to confirm his identity through fingerprints. Also inside the crypt were the boxes of bones, according to investigators on the scene.
The church has been used for burials for two centuries. Still, all of the bones will be tested to determine whether they are tied to De Pedis or to Emanuela's disappearance.
De Pedis will not be reburied in the church, the Vatican said.
De Pedis family lawyer Lorenzo Radogna said the remains will either be cremated or reinterred in a public cemetery in Rome.