A Ugandan court has found Thomas Kwoyelo, the only commander of the feared Lord’s Resistance Army (LRA) to be tried in the East African country, guilty of multiple counts of crimes against humanity.

“He is found guilty of the 44 offences and hereby convicted,” lead Judge Michael Elubu said on Tuesday at the International Crimes Division (ICD) of the High Court in the northern city of Gulu, where the LRA was once active.

He added that Kwoyelo was found not guilty of three counts of murder, and that “31 alternate offences” were dismissed.

His offences included murder, rape, torture, pillaging, abduction, and destruction of settlements for internally displaced people, the judge said.

It was not immediately clear when Kwoyelo would be sentenced.

It was the first atrocity case to be tried under a special division of the High Court that focuses on international crimes.

Kwoyelo, who was abducted by the LRA at the age of 12, had denied all the charges against him.

A low-level commander in the militia, Kwoyelo was arrested in March 2009 in the Democratic Republic of Congo (DRC) during a sweep by regional forces against LRA rebels who had fled from Uganda two years earlier.

He was put on trial in July 2011 before the ICD but was freed two months later on the orders of the Supreme Court, which said he should be released on the same grounds as thousands of other fighters who were granted amnesty after surrendering.

But the prosecution appealed the decision and he was put on trial again, though the case was repeatedly delayed.

The LRA was founded by former altar boy and self-styled prophet Joseph Kony in Uganda in the 1980s with the aim of establishing a regime based on the Ten Commandments.

Its rebellion against President Yoweri Museveni saw more than 100,000 people killed and 60,000 children abducted in a reign of terror that spread from Uganda to Sudan, the DRC, and the Central African Republic.

Kony is wanted by the International Criminal Court for rape, slavery, mutilation, murder and forcibly recruiting child soldiers. The US has offered $5m as a reward for information leading to his capture.

Thousands of rebel combatants have received Ugandan government amnesty over the years, but Kwoyelo was denied such a reprieve.

Ugandan officials have never explained why. There were concerns by rights activists that the long delay in trying him violated his right to justice.

Kwoyelo’s trial was controversial, underscoring complex challenges in delivering justice in a society still healing from the consequences of war.

The defendant maintained that he was abducted as a young boy to join the ranks of the LRA and that he could not be held responsible for the group’s crimes.

Kwoyelo, who denied the charges against him, testified that only Kony could answer for LRA crimes, and said everyone in the LRA faced death for disobeying the warlord.