Several people died and around 1,000 others were wounded when police and miners attacked demonstrators in Bucharest in June 1990.
Ion Iliescu, 85, was president from 1990 until 1996 and then returned for a second term from 2000 to 2004.
He was accused of murder in 2005.
However, those charges were dropped two years later and he has always rejected the allegations against him as absurd.
In September 2014, the European Court of Human Rights criticised Romania's failure to put on trial people responsible for "crimes against humanity committed against Romanian civilians in the tortuous transitional period to democracy".
The Romanian Supreme Court then re-opened the case in March 2015.
Mr Iliescu made no comment in court as he appeared with other former government officials, including ex-intelligence director Virgil Magureanu and ex-Defence Minister Victor Atanasie Stanculescu.
Months before he became president, Mr Iliescu helped bring down the Communist regime of Nicolae Ceausescu.
However, when opposition protesters took to the streets to voice their anger against the new ex-Communist leadership, their demonstration was broken up by thousands of miners sent to Bucharest by Mr Iliescu to stage a counter-protest.
Romanian TV broadcast archive footage of Mr Iliescu on Wednesday, showing him thanking the miners for coming to the new government's help.
Former miners' leader Miron Cozma led the miners when they broke up the opposition protest in 1990 but led a miners' march on Bucharest the following year which helped bring down the government.
He was later jailed for his role in the 1991 miners' actions.
Romania's ex-President Ion Iliescu is facing prosecution on charges of crimes against humanity for the violent suppression of a protest months after the fall of the Communist regime.