The charges relate to the country's civil conflict that erupted after Mr Gbagbo lost elections in 2010.
Prosecutors accuse him of orchestrating a "campaign of violence".
Mr Gbagbo, 70, and ex-militia leader Charles Ble Goude, 44, deny murder, rape, attempted murder and persecution.
The trial at the court in The Hague, in the Netherlands, could last three or four years.
Inside the courtroom, Laurent Gbagbo seemed unsteady, leaning on his desk as he pleaded not guilty. His co-accused, Charles Ble Goude, gave a more defiant response, telling the judges: "I do not recognise the charges."
Prosecutors said Mr Ble Goude had acted as a spin doctor. He called himself the "street general". Archive footage played in court showed him comparing himself to former British Prime Minister Tony Blair's media adviser Alastair Campbell.
Chief prosecutor Fatou Bensouda used her opening statement to focus on the victims. She spoke of one woman who was arrested during a peaceful march in Abidjan and detained for three days. During that time, Ms Bensouda said, the woman was gang-raped by police officers - the very people who were supposed to protect her.
Outside protesters playing on bongo drums complained of "victor's justice". To date none of President Alassane Ouattara's supporters have been charged by the ICC.
Mr Gbagbo sparked a crisis in Ivory Coast after he refused to step down following his loss to Alassane Ouattara in the 2010 presidential vote.
There were bloody clashes between rival forces over five months in 2010 and 2011.
Some 3,000 people were killed, with Mr Gbagbo basing himself in the presidential palace.
He was arrested in April 2011 by forces loyal to President Ouattara, backed by troops from former colonial power France, and later that year was extradited to The Hague.
It will be the highest-profile trial yet for the ICC, which has only convicted two Congolese warlords since its establishment in 2002.
Reading out the charges, prosecutors cited cases including the alleged rape of 38 women at a pro-Ouattara rally and alleged killing of 10 people by shelling at a market.
The prosecution said it currently planned to bring forward 138 witnesses.
Chief prosecutor Fatou Bensouda said that when Mr Gbagbo "understood that the presidency was going to escape him... he began a campaign of violence orchestrated against those considered opponents".
"Nothing would be allowed to defeat Mr Gbagbo, and if politics failed, violence was seen as politics by other means," she said.
Presiding Judge Cuno Tarfusser said neither Ivory Coast nor its people were on trial, and that he would not allow the court to be used as a "political instrument".
Dozens of Gbagbo supporters gathered outside the ICC on Thursday to back the ex-president, sparking some scuffles with police.
"Our dream to see our president walk free starts today," said one supporter, Marius Boue. "He is truly a man of the Ivorian people"
Gbagbo: From professor to president
Image copyrightReutersImage captionMr Gbagbo was arrested with his wife Simone in 2011; she would later be sentenced to 20 years in jail by an Ivory Coast court
Born in 1945, Mr Gbagbo's first career was in academia as a history professor
He was jailed for two years in 1971 for "subversive" teaching
By the 1980s, he was heavily involved in trade union activities
After years in exile, he returned to Ivory Coast to attend the founding congress of the Ivorian Popular Front in 1988
Mr Gbagbo was one of the first to challenge Ivory Coast's founding President Felix Houphouet-Boigny, after multi-party politics were permitted
Became president with the Ivorian Popular Front in 2000
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