The man portrayed as a hero in a Hollywood movie about the Rwandan genocide has been charged with terrorism, murder and other crimes.
Paul Rusesabagina declined to enter any pleas in court but his lawyers denied the charges against him.
Mr Rusesabagina is the leader of the opposition MRCD group which is said to have an armed wing, the FLN, which stages attacks on Rwanda.
He was brought to the court under heavy security in Rwanda's capital, Kigali.
Mr Rusesabagina is a fierce critic of President Paul Kagame and had been living abroad.
An ethnic Hutu, he became well known after the 2004 film Hotel Rwanda depicted his efforts a decade earlier during the genocide to save hundreds of Tutsis at a hotel where he was a manager.
Paul Rusesabagina's family allege the political exile was kidnapped in Dubai earlier this month and taken to Rwanda.
Mr Rusesabagina, who is also a Belgian citizen and a US green-card holder, left his home in San Antonio, Texas, and landed in Dubai at the end of August, his family told the BBC.
"We believe he was kidnapped because he would never go to Rwanda on his own will," his daughter told the BBC.
Rwandan officials said Mr Rusesabagina, 66, was arrested under an international warrant for leading "terrorist movements".
Why was he charged now?
Mr Rusesabagina's name featured recently in a terrorism case in Rwanda. The court had heard allegations that the National Liberation Front (FLN) rebel group had received help from Zambia's President Edgar Lungu because of his close friendship with Mr Rusesabagina.
Mr Lungu's spokesman denied the allegation in a BBC interview.
In 2011, Mr Rusesabagina was accused of funding subversion in Rwanda, but no charges were brought.
At the time, he denied any wrongdoing and said there was a smear campaign against him.
President Kagame's critics accuse him of not tolerating any opposition. Several opposition leaders have been jailed and others fled into exile. Mr Kagame says he is trying to prevent a return of ethnic hatred.
What is Hotel Rwanda about?
The 2004 film Hotel Rwanda told the story of how Mr Rusesabagina, a middle-class Hutu married to a Tutsi woman, used his influence - and bribes - to convince military officials to secure a safe escape for an estimated 1,200 people who sought shelter at the Mille Collines Hotel in Kigali.
Don Cheadle played Mr Rusesabagina in the film.
Rwandan genocide survivors' group Ibuka has in the past said that he exaggerated his own role in helping hotel refugees escape the 100-day slaughter.
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In 2007, Mr Rusesabagina said a UN-backed war crimes court should put some members of the Rwandan Patriotic Front - the rebel group led by President Kagame which took power and ended the genocide - on trial for their alleged role in the 1994 killings.
"I'm just a normal person. But I've always defended human rights," he said at the time.
"I'm trying to be the voice of millions of Rwandese who have no-one to speak out for them."