Human rights advocates have said the prosecution of Jose Efrain Rios Montt would be an important symbolic victory for the victims of one of the most horrific of the conflicts that devastated central America during the last decades of the Cold War.
Rios Montt is the first former President to be charged with genocide by a Latin American court.
Paul Seils, vice-president of the New York-based International Centre for Transitional Justice, which has worked on war-crimes cases in Guatemala, said: "It's the beginning of a new phase of this struggle."
He said the decision to prosecute was a good step forward but expected the case to encounter resistance from groups in Guatemala opposed to the punishment of government-allied forces for their actions during the civil war.
Others hailed the judge's ruling as a less-qualified victory for justice in Guatemala.
Jose Miguel Vivanco, Americas director at Human Rights Watch, said: "The fact that a judge has ordered the trial of a former head of state is a remarkable development in a country where impunity for past atrocities has long been the norm."