Compaore and 12 others face charges of harming state security, complicity in murder and complicity in the concealment of corpses.
Among those accused alongside Compaore is General Gilbert Diendere, Compaore's former right-hand man and a former head of the elite Presidential Security Regiment (RSP) at the time of the coup.
Diendere is already serving a 20-year sentence in Burkina Faso for masterminding a plot in 2015 against the West African country's transitional government. He is believed to have headed the unit that killed Sankara.
Several other members of the presidential guard at that time will also join them in the dock. However, 34 years after the events in question some of those originally accused have already died, according to lawyers for the plaintiffs in the case.
Compaore in exile
Sankara took power in a coup in 1983, but was killed on October 15, 1987, when he was 37, in a putsch led by Compaore.
Compaore was himself ousted in 2014 by a popular uprising after 27 years in power.
He has always denied ordering Sankara's murder, but even mentioning Sankara's name was taboo in Burkina Faso under his rule.
A warrant was issued for Compaore's arrest during the transitional government in March 2016 .
Now 70, Compaore currently lives in Cote d'Ivoire, where he fled after being ousted and where he has since taken citizenship.
Unless he chooses to present himself for trial, he will be judged in absentia.
Published/Updated on 10/[email protected]:21