Presiding judge Nil Nonn said the first hearing represented "the realisation of significant efforts to establish a fair and independent tribunal to try those in leadership positions and those most responsible for violations of Cambodian and international law".
But Francois Roux, for the defence, said it was "unacceptable" Duch had been held without trial for more than nine years.
The first days are mainly procedural, with witness testimony expected to be heard only during hearings next month, says the BBC's South East Asia correspondent, Jonathan Head.
Duch was driven by bulletproof car from a detention centre to the specially-built court-room.
Duch (left) ran a Khmer Rouge prison where almost all inmates were killed
He is one of five former Khmer Rouge leaders who will face trial and is unusual in that he has expressed regret for what he did, and asked the forgiveness of his victims.
He wanted another chance to express his remorse, Mr Roux told reporters.
"Duch wishes to ask forgiveness from the victims but also from the Cambodian people. He will do so publicly. This is the very least he owes the victims."
The courtroom was packed with people, many of them survivors of the Khmer Rouge or relatives of victims of the regime.
"It was really amazing to see victims of Duch sitting there in front of him in a courtroom confronting their perpetrator of 30 years ago," said Theary Seng, the director of the Centre for Social Development in Phnom Penh.
Her parents were killed by the Khmer Rouge and she spent five months in prison as a child.
"I'm certain there was satisfaction and I'm certain there was a large degree of empowerment," she told the BBC.
Duch, a former teacher, was commander of the Tuol Sleng interrogation centre, also known as S-21, in the capital Phnom Penh for four years after the Khmer Rouge victory in 1975.
He is accused of personally overseeing the systematic torture of more than 15,000 prisoners.
Those who survived the ordeal were sent for execution in the so-called "killing fields".
KHMER ROUGE YET TO FACE TRIAL
Khieu Samphan: former president
Ieng Sary: foreign minister
Ieng Thirith: minister for social affairs (and wife of Iengy Sary)
Pol Pot, the founder and leader of the Khmer Rouge, died in a camp along the border with Thailand in 1998, the same year his few remaining guerrillas agreed to finally abandon their fight.
As many as two million people are thought to have died from starvation, overwork and execution as the Khmer Rouge emptied the cities to send people to work on collective farms during its four years in power.
Cambodia originally asked the United Nations and international community to help set up a tribunal into the genocide more than a decade ago.
A joint tribunal was finally set up in 2006 following long drawn-out negotiations between the Phnom Penh government and the UN.
Bail hearings, appeals and pre-trial procedures have contributed to further delays.
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