He faces six counts including premeditated murder, gucci shoes 2012 bomb-making and illegal firearms possession.
Patek is believed to be a key member of Jemaah Islamiah (JI), the militant Islamist group blamed for the attacks and linked to al-Qaeda.
He was arrested in January 2011 in Abbottabad, Pakistan, where Osama bin Laden was later killed.
In August he was extradited to Indonesia in a move seen at the time as a significant coup for anti-terror agencies in the country.
The trial is expected to go on for months, says the BBC's Indonesia Correspondent, Karishma Vaswani. A verdict would likely be delivered at the end of May or in early June.
Security analysts believed it was no coincidence that he was caught in the same town as where the former al-Qaeda leader was hiding, but officials could not confirm whether the two had met.
Bin Laden was killed in a raid by United States forces in May 2011.
No terrorism charges
There were between 260 to 300 police guarding the court, markedly less than the security provided for the trial of Abu Bakar Bashir, the radical cleric seen as the spiritual leader of JI.
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At the scene
BBC News, Jakarta
Umar Patek is thought to be one of the last high profile members of the group behind the Bali blasts.
The attack was the worst ever on Indonesian soil, gucci bags 2012 killing more than 200 people.
Bringing him to trial is seen as a significant victory for Indonesia's anti-terror forces. But analysts say it is unlikely his trial will mean much for Indonesia's fight against terror.
The country has faced other, smaller, more sporadic attacks over the last few years.
There is a new strain of militancy in Indonesia. Although the apparent goal is very much the same - to turn Indonesia into an Islamic state - the targets are no longer necessarily foreign, but often local officials and minorities instead.
But authorities say they are not being complacent, says our correspondent.
Prosecutors have said that they will push for the maximum death penalty but some analysts think he could be given a life sentence instead.
The attack in 2002 on the Indonesian island took place at Paddy's Bar and Sari Club in the resort of Kuta. It was targeted mostly at foreigners. Those killed were from 21 countries, including 88 Australians, 38 Indonesians and 28 Britons.
Patek is not facing terrorism charges, but that of premeditated murder, because the terrorism law came into effect in Indonesia in 2003. The law cannot be applied retrospectively.
Patek, who appeared in court in a white robe, will also face charges for his alleged role in church bombings in Jakarta in 2000, which killed at least 19 people.
According to a court document obtained by the AFP new agency, he fled to the Philippines after the attacks in Bali, and joined the rebel Moro Islamic Liberation Front (MILF) there, gucci shoes outlet with the intention of going to Afghanistan.