Brazil's Human Rights Ministry says on its website there are suspicions he was poisoned.
Those suspicions stem from statements made in 2008 by a former Uruguayan intelligence officer imprisoned in Brazil for drug smuggling. He told the Folha de S. Paulo newspaper that Goulart had been poisoned by agents of Operation Condor, under which the military dictatorships that ruled much of South America in the 1970s and 1980s secretly cooperated in the torture and disappearances of each others' citizens.
The Uruguayan agent told the newspaper that Goulart's heart medication had been swapped with poisoned pills that caused a heart attack.
"We are taking the first big step to tell the truth that for many years has been omitted," the Truth Commission's website quoted Goulart's son, Joao Vicente, as saying.
Justice Minister Jose Eduardo Cardozo said, "Families have the right to know how their loved ones died and a country's citizens have the right to know how their leaders died."
Goulart served as vice president during the governments of Juscelino Kubitschek and Janio Quadros.
In 1961, Quadros resigned and Goulart assumed the presidency. His term was marked by greater investments in education, agrarian reform and higher taxes on the wealthy.
Goulart's exhumation was authorized in 2012 by a federal court.
The Human Rights Ministry said Goulart's remains will be taken to Brasilia to be examined by Brazilian Argentine and Uruguayan forensic experts. There he will be given full state honors, which he did not receive when he was buried. His body will be returned to Sao Borja on Dec.6
The toxicology tests needed to determine if Goulart's was poisoned will be conducted outside Brazil the Human Rights Ministry said without revealing where.