Ex-general Benedicto Lucas García, 91, has been indicted for genocide, crimes against humanity - including widespread rape - and forced disappearances.
The former general was accused of ordering the murder of more than 1,200 indigenous Ixil Maya people during Guatemala's civil war.
The alleged crimes occurred between 1978 and 1982, when Lucas García's brother Fernando Romeo Lucas García was president of Guatemala.
For seven months between 1981 and 1982, Lucas Garcia helmed Guatemala’s forces, as part of the administration of President Romeo Lucas Garcia, his brother. He now stands accused of genocide, crimes against humanity, forced disappearances and sexual violence.
A United Nations-backed truth commission found that the military committed acts of genocide against five of the country’s 22 different Maya peoples between 1981 and 1983. That period overlaps with Lucas Garcia’s tenure as the chief of the general staff of the army.
Benedicto Lucas García is accused of planning and executing over 30 massacres in the western region of Quiche.
Lawyer Nery Rodenas, director of the Human Rights Office of the Archbishopric of Guatemala, told the AFP news agency that survivors had waited "more than 40 years" for justice.
Many Ixil Maya people were targeted by the military, accused of providing support to Marxist rebels.
Some 200,000 people died in the conflict, which lasted almost 40 years. Most were ethnic Maya.
Guatemala's Supreme Court of Justice ruled in 2018 that acts of genocide had been committed against the Ixil people. But only a small number of low-ranking soldiers have been convicted of war crimes.
In 2013, Guatemala made history when a court convicted Rios Montt of genocide. But the verdict was overturned soon after in a widely-questioned ruling, illustrating the difficulties of prosecuting such a case.
Rios Montt died before a partial retrial could end in 2018. On September 27 of that year, a tribunal ruled the military did commit genocide, but no one was convicted.
Advocates, however, emphasise that the atrocities perpetuated by Rios Montt and others extended beyond the Mayan Ixil people, also targeting other Indigenous peoples, unions, clergy, student movements and other groups.
For example, in a separate case from 2018, Lucas Garcia was convicted of rape, forced disappearance, and crimes against humanity for actions taken against an activist and her family. He was sentenced to 58 years in prison.
