Officials hope that a forensic analysis of Allende's remains will resolve a decades-old controversy over his death in his presidential palace on September 11, 1973 in the midst of the coup that brought General Augusto Pinochet to power.
The official version was that Allende killed himself with an assault rifle -- a gift from Cuban leader Fidel Castro -- as the La Moneda presidential palace was being bombed by Air Force planes and besieged by tanks and soldiers.
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But neither the weapon nor bullets were recovered following his death, and Pinochet's military regime prevented Allende's family from seeing his corpse after the coup. There was no criminal investigation into his death.
A Chilean prosecutor announced the inquiry in January, part of an investigation into 725 unresolved human rights complaints against Pinochet's 1973-1990 military dictatorship.
Members of Allende's family and International Red Cross representatives were on hand as workers broke open the family mausoleum at the Santiago General Cemetery and brought out a casket.
Experts carried out some preliminary work at the site, then sent the remains to the Legal Medical Service office to be analyzed by a team of Chilean and foreign experts, including specialists in ballistics and forensic odontology.
"This legal process seeks to establish the truth about what happened on that tragic September 11, 1973, and especially the circumstances surrounding the death of president Allende," said the late president's daughter, Senator Isabel Allende.
Most supporters, including family members, claim Allende chose to commit suicide rather than surrender and be forced to resign. However Fidel Castro, other leftist leaders and some media outlets maintain that Allende was killed by oncoming soldiers.
An autopsy by the military regime established that Allende committed suicide by placing the gun under his chin and pulling the trigger.
However Luis Ravanal, a forensic doctor who reviewed the autopsy material in 2008, said that the data showed two bullet wounds, which he said was incompatible with a suicide.
The condition of Allende's remains will be key to finding an answer, said Patricio Bustos, head of the Legal Medical Service office. As a first step the bones will be X-rayed, Bustos said.
Justice Minister Felipe Bulnes said the government of President Sebastian Pinera -- who heads the first conservative administration since democracy was restored in 1990 -- supports the probe "for the sake of the family as well as the country."
The leftist Allende was elected president of Chile in 1970. He was 65 at the time of his death.
Allende was warned of an impending coup on the morning of September 11, and showed up at the presidential palace dressed in a suit, wearing a helmet and carrying a rifle to coordinate the resistance, witnesses said.
Chile is also probing the 1982 death of former president Eduardo Frei Montalva, who preceded Allende in office.
Frei, president from 1964-1970, was emerging as a strong opponent to the Pinochet dictatorship when he was allegedly poisoned and died after visiting a hospital to treat a hernia.
In December 2009, six people -- the ex-leader's driver, his personal assistant and four doctors -- were charged in the case.
