They are accused of being part of a nationalist network called Ergenekon - which takes its name from a legendary valley in central Asia believed to be the ancestral homeland of Turks - or of plotting an armed uprising.
The courtroom can accommodate about 280 people, but an accreditation system appeared to have failed.
"The trial is being held in a courtroom too small and inappropriate for a fair trial," Sahin Mengu, an opposition politician, said outside the court. "This is the Turkish republic's shame."
The court will now first hear the testimonies of the 46 suspects that have been remanded in custody, before the remaining 40 other give testimony in separate hearings
"I have been doing this job for 30 years and never saw such conditions," one lawyer said.
Hundreds of people had gathered outside the courthouse in support of the defendants, holding Turkish flags and portraits of the suspects.
Many of the suspects are known as fierce opponents of the government of Recep Tayyip Erdogan, the prime minister.
"I don't deny the existence of Ergenekon or other criminal organisations. But the trial has lumped real criminals with innocent people..."
Tafan Turance, columnist with the Hurriyet newspaper
They organised anti-government rallies attended by hundreds of thousands of secular Turks.
Mohamed Vall, Al Jazeera's correspondent in Istanbul, said the case had caused great intrigue and many consider it as the biggest trial in Turkey's modern history.
"The plotters are accused of attempting to create a state of chaos through rumours, explosions and assassinations, all in order to instigate a military coup," Vall said.
"The gang's action manual included a list of non-Islamist politicians and intellectuals slated for assassination, among them the Nobel laureate Orhan Pamuk.
"They have been charged with some of Turkey's most notorious murders.
"But the biggest shock came in July, when some former high ranking military officials were arrested for possible links to the secret organisation, including Sener Eruygur, a former force commander, and general Hursit Tolon, a former commander of the 1st Army Corps."
Vall said many people believed the trial would take months, if not years to complete.
The trial has stoked rivalries between supporters of Erdogan and secularists, who say the inquiry is occurring to intimidate and silence opponents.
Once the hearing got under way on Monday, defence lawyers demanded that judges be replaced, or that the entire case be dismissed, saying that it was politically motivated.
"This trial is not a legal trial, it is a political trial led for the alliance between Erdogan and [US President] George W. Bush," Nevzat Erdemir told the court.
Kemal Kerincsiz, a lawyer who is one of the defendants, said that the trial was launched "against patriots" by those "who want to install a moderate Islamist regime and a federation in Turkey".
The military has ended the rule of four governments in four decades in Turkey. Many secularists suspect Erdogan's Justice and Development Party (AKP) of pushing a secret plan to install Islamic rule in the country.
Tafan Turance, a columnist with the Hurriyet newspaper, told Al Jazeera: "This has become a politicised case, which destroys its legal value.
"I don't deny the existence of Ergenekon or other criminal organisations. But the trial has lumped real criminals with innocent people who are opposed to the government in this case"
Erhan Celik, a presenter with Channel 7 TV station, said that it was time that renegade members of the army and security forces - known as the ‘Deep State' in Turkey - were brought to account.
He said: "This case is not a debate between seculars and anti-seculars. In fact it's an instance of the battle between supporters of democracy and those who oppose it."
The suspects were arrested after an investigation into the discovery of hand grenades in Istanbul in June 2007.