The Guatemalan government, using the Guatemalan Army and its counter-insurgency force (whose members defined themselves as 'killing machines'), began a systematic campaign of repressions and suppression against the Mayan Indians, whom they claimed were working towards an communist coup.
Their 2-year series of atrocities is sometimes called 'The Silent Holocaust'.
In the words of the 1999 UN-sponsored report on the civil war: 'The Army's perception of Mayan communities as natural allies of the guerrillas contributed to increasing and aggravating the human rights violations perpetrated against them, demonstrating an aggressive racist component of extreme cruelty that led to extermination en masse of defenceless Mayan communities, including children, women and the elderly, through methods whose cruelty has outraged the moral conscience of the civilised world.'
Working methodically across the Mayan region, the army and its paramilitary teams, including 'civil patrols' of forcibly conscripted local men, attacked 626 villages. Each community was rounded up, or seized when gathered already for a celebration or a market day. The villagers, if they didn't escape to become hunted refugees, were then brutally murdered; others were forced to watch, and sometimes to take part. Buildings were vandalised and demolished, and a 'scorched earth' policy applied: the killers destroyed crops, slaughtered livestock, fouled water supplies, and violated sacred places and cultural symbols.
Children were often beaten against walls, or thrown alive into pits where the bodies of adults were later thrown; they were also tortured and raped. Victims of all ages often had their limbs amputated, or were impaled and left to die slowly. Others were doused in petrol and set alight, or disembowelled while still alive. Yet others were shot repeatedly, or tortured and shut up alone to die in pain. The wombs of pregnant women were cut open. Women were routinely raped while being tortured. Women - now widows - who lived could scarcely survive the trauma: 'the presence of sexual violence in the social memory of the communities has become a source of collective shame'.
Covert operations were also carried out by military units called Commandos, backed up by the army and military intelligence. They carried out planned executions and forced 'disappearances'. Death squads (some of which in time came under the army's umbrella), largely made up of criminals, murdered suspected 'subversives' or their allies; under dramatic names, such as 'The White Hand' or 'Eye for an Eye', they terrorised the country and contributed to the deliberate strategy of psychological warfare and intimidation.
URNG's guerrillas could not provide assistance to the Mayan Indians: there were too few of them. There were certainly too few to be a real threat to the State, whose massive and brutal campaign was largely driven by long-term racist prejudice against the Mayan majority. Of the human rights violations recorded, the State and the Army were responsible for 93%, the guerrillas for 3%.
Throughout the period of the genocide, the USA continued to provide military support to the Guatemalan government, mainly in the form of arms and equipment. The infamous guerrilla training school, the School of the Americas in Georgia USA, continued to train Guatemalan officers notorious for human rights abuses; the CIA worked with Guatemalan intelligence officers, some of whom were on the CIA payroll despite known human rights violations. US involvement was understood to be strategic - or, put another way, indifferent to the fate of a bunch of Indians - in the wider context of the Cold War and anti-Communist action.