Karpeles, 32, has pleaded not guilty to charges of falsification of information and embezzling 321 million yen (2.4 million euros) when he was boss of the Tokyo-based MtGox company.
"I swear before God that I am innocent," he told the court and went on to read a letter in Japanese written by his lawyer.
The reading of the charges in Japanese then in French took an hour in total, so long that the judge allowed the defendant to sit down.
Karpeles, who was helped by two Japanese interpreters, claimed that MtGox was a victim of a cyberattack.
"MtGox's bankruptcy caused a lot of damage and, as its CEO at the time, I present my apologies," he said.
About 100 people, among them people who had lost money they invested in the country, tried to attend the first day of the trial but only 21 were able to after being picked by drawing lots.
Those who have lost money could be compensated in whole or in part, according to the Japanese media.
Karpeles, who was arrested in September 2015, imprisoned and then released on bail a year ago, has already been found guilty of online hacking.