Emanuela Orlandi, the daughter of a Vatican employee, was last seen leaving a music class in 1983. She was 15 years old.
There was nothing found in the two graves opened in the Teutonic Cemetery on Thursday, according to the Vatican.
One grave was "completely empty" while the other had no human remains, spokesman Alessandro Gisotto said in a statement.
The disappearance of Emanuela fueled numerous conspiracy theories, with accusers pointing the finger at the Italian mafia, sexual predators within the clergy, and foreign intelligence agencies.
Her older brother Pietro has kept up public pressure on Vatican officials over the years. Family lawyer Laura Sgro reported receiving an anonymous letter earlier this year with a photo of an angel on a Vatican cemetery, and a message that read "Look where the angel is pointing."
The site turned out to be Vatican's Teutonic Cemetery, a small graveyard beyond St. Peter's Basilica which serves as a resting place for German and Flemish-speaking Vatican residents. The cemetery is off limits to tourists.
Decades of inquiryBased on the photo, Vatican officials decided to open the graves of two princesses, one of whom was buried there in 1836 and another in 1840.
Pietro Orlandi, who is now 60 years old, said some people in the Vatican might have been involved in his sister's disappearance.
"I've always hoped she's alive, and to find her alive," he said before the graves were opened. "But if Emanuela is dead and is buried there, it's right that what has been hidden for so many years comes to light."
jm,dj/ng (AFP, dpa)
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