The LRA is noted for kidnapping children and forcing the boys to fight as soldiers and using girls as sex slaves.
It is also accused of killing, kidnapping and mutilating tens of thousands of people across central Africa since the late 198O's.
The trial against Thomas Kwoyelo opened at Uganda's International War Crimes Division under tight security in Gulu yesterday.
Kwoyelo denied 53 counts of murder, hostage-taking, destroying property and injuring people.
He is also accused of heading up a 1996 attack on a Congolese village, where residents were forced to carry things the rebels had stolen. "Those who failed were summarily executed," the charge sheet said, according to Agence France Presse.
"The rebels brutally tortured the women. The accused then ordered his forces to kill all the elderly captives."
The court, in the north of the East African country, was set up after peace talks between the government and the LRA. The government promised the LRA that its fighters would be given amnesty or they would be tried by Ugandan courts, rather than the International Criminal Court, but Kwoyelo was denied amnesty.
"Domestic war crimes prosecutions are essential to ensuring perpetrators of serious crimes committed during the conflict in northern Uganda do not escape justice," said Human Rights Watch lawyer Elise Keppler. "But trials must be fair and credible and witnesses need adequate protection. This first trial before the International Crimes Division will test whether these standards are being met," she said.
The LRA says it is fighting for a biblical state and the rights of the northern Acholi people. The Ugandan army has been trying to stamp down a rebellion in the north for longer than 20 years. The rebels now operate mostly in small groups, attacking and looting villages across the region.
Last month, 39 aid groups warned that the LRA is still terrorising communities in Congo, the Central African Republic and South Sudan.
Three LRA leaders - Joseph Kony, Okot Odhiambo, and Dominic Ongwen - are wanted by the International Criminal court for war crimes and crimes against humanity.
Uganda was known for its human rights abuses, in the 1970s and 80s, first during the military dictatorship of Idi Amin from 1971-79 and then after the return to power of Milton Obote, who had been ousted by Amin. In this space of time, up to half a million people were killed in state-sponsored violence.