There are 17 indigenous tribes in Paraguay with the majority having their territories in the Chaco region. Tribes in this region include the Guaraní, Ayoreo, Toba-Maskoy, Aché and Sanapan which according to the census from 2002 number an estimated 86,000 or roughly around 2 per cent of the total population. Between 1956 and 1989 while under the military rule of General Alfredo Stroessner the indigenous population had more territory taken than at any other period in Paraguay's history and were subjected to systematic human rights abuses. In 1971, Mark Münzel, a German anthropologist accused Stroessner of attempted genocide against the indigenous peoples of Paraguay and Bartomeu Melià, a Jesuit anthropologist stated that the forced relocations of the indigenous peoples was ethnocide. In the early 1970s the Stroessner regime was charged by international groups of being complicit in genocide. However, because of the repressive actions undertaken by the state the indigenous tribes organized themselves politically and had a major role in bringing about the end of the military dictatorship and the eventual transition to democracy.
During the 1960s and 1970s, 85 per cent of the Aché tribe died, with many hacked to death with machetes to make room for the timber industry, mining, farming and ranchers. According to Jérémie Gilbert, the situation in Paraguay has proven that it is difficult to provide the proof required to show "specific intent", in support of a claim that genocide had occurred. The Aché, whose cultural group is now seen as extinct, fell victim to the development by the state, who had promoted the exploration of Aché territory by transnational companies for natural resources. Gilbert concludes that though planned and voluntary destruction had occurred, it is argued by the state that there was no intent to destroy the Aché, as what had happened was due to development.
The allegation of genocide by the state was brought before the Inter-American Human Rights Commission which has jurisdiction on allegations of genocide carried out by a state. The commission gave a provisional ruling that Paraguay had not carried out a genocide, but stated it had concerns over "possible abuses by private persons in remote areas of the territory of Paraguay".