Ms Choi was a close confidante of impeached President Park Geun-hye.
Prosecutors say Ms Choi used their relationship to pressure companies to donate to two foundations, and siphoned off money for personal use.
The case has prompted nationwide outrage and a vote by parliament earlier this month to impeach Ms Park.
Ms Choi's appearance in court, for a preliminary hearing before her trial begins, was the first time she had been seen in public since October.
Though she was not required to attend the hearing, her lawyers said she had volunteered to appear.
They said she wanted the truth to emerge with clarity, and that she denied all charges.
Ms Choi said: "I'm sorry for causing trouble. I'll faithfully engage in [my] trial."
The BBC's Stephen Evans, in Seoul, said she appeared calm and collected in court.
A parliamentary inquiry this month saw business leaders admit that their firms gave money to Ms Choi's foundations, with one company - Samsung - confirming that they paid for a gift horse for Ms Choi's daughter, a professional equestrian.
It denied that it had done so to seek favours with Ms Park, but some firms acknowledged it was difficult to refuse government requests.
Ms Park herself has been accused of playing a role in the corruption case, which she has strongly denied.
She has, however, admitted to giving Ms Choi inappropriate government access, including to her presidential speeches, and has apologised several times.
The case has sparked immense public anger in South Korea, prompting large demonstrations calling for Ms Park to step down.
The impeachment vote suspended Mr Park from presidential duties while the country's constitutional court considers the motion.
Hwang Kyo-ahn, the country's prime minister, has become interim president.
The woman at the centre of South Korea's political crisis, Choi Soon-sil, has appeared in court, where she denied charges of corruption.