They are accused of "attempting to destroy the constitutional order" and "murder", state-run Anadolu news agency reported.
They are also charged with "membership of an armed terror group" and "forming and running a terror group," said the indictment. The grave offences mean a potential record jail term -- up to 3,342 years -- if convicted.
Anadolu said 42 of the accused, who had been under arrest, appeared in court at Silivri, outside Istanbul, in a hearing due to last four days. The other four suspects remain at large.
Those killed in the suicide bombings at Ataturk Airport on June 28, 2016, included 19 foreigners and it was one of the worst attacks to rock Turkey's biggest city that year.
More From This Section
No group has claimed responsibility for the attack but Turkey says the Islamic State group was behind the airport blasts. The court indictment also said IS "targeted the Turkish republic."
Two of the three assailants in the massacre were identified as Rakim Bulgarov and Vadim Osmanov, according to court papers which did not identify the third attacker.
Turkish media had previously identified the man who organised the attack as Akhmed Chatayev, the Chechen leader of an IS cell in Istanbul who reportedly found accommodation for the bombers.
The attackers had scouted the airport three times, on June 3, 8 and 23, according to the indictment.
Turkey has been hit by several bloody attacks blamed on IS militants over the past two years, including a New Year attack this year on a Istanbul nightclub in which 39 people were killed.