This paper argues that systematic acts of violence in Indonesia only began to occur during the time of Dutch colonial rule and increased in scale in the post-Independence period when the number of victims of the violence of 1965 was greater than during the whole period prior to Independence. The tragedy which took at least half a million lives was the biggest act of violence in the history of Indonesia and has had widespread repercussions in terms of human rights, the repressive role of the state, and further acts of state-perpetrated violence for the following four decades. It also overlapped with inter-communal violence where community groups were coerced or willingly assisted in the killing of alleged members of the communist party. According to some definitions, the events of 1965-66 can be considered an act of genocide consisting of the partial destruction of a group in society similar to the act of killing the intellectual elites of Cambodia. Reconciliation has been effected at the local level in recent times, with notable efforts taking place between Muslim groups and the victims of the violence. However, such reconciliation needs to take on national proportions through active investigations as a part of a Truth and Reconciliation Commission.