Most of the architects of the slaughter got away to Europe, the United States or other African countries. Tens of thousands of their followers - members of the interahamwe Hutu militia - spent the intervening years in refugee camps all over central Africa, awaiting the orders to return and complete the genocide, wiping out the existing Rwanda government.
These men are now the front-line forces of the president of the Congo republic, Laurent Kabila, as he fights opponents seeking to oust him - a conflict that has drawn in several neighbouring states and has become in part a fresh phase of the genocide of 1994.
But in Rwanda during the past five years the people have moved on with a determination no outsider could have forecast after the traumatic three months of mass killing. Two days of voting for village leaders last week brought an 80 per cent turn-out in rural areas and 75 per cent in urban areas. For the first time since Rwanda's independence from Belgium in 1962 voting was not obligatory. No one was allowed to campaign on ethnic, religious or political grounds.
'This is the first time people are free to put forward as a candidate and elect whomsoever they like, Hutu or Tutsi,' said Charles Karake, the mayor of Kigali.
The elections followed a series of weekly consultative meetings between President Pasteur Bizimugu and a wide cross-section of community and political leaders. Regional and national elections are to follow.
Ruhengeri, in the north-west of the country, is a touchstone of the change. Here, on the edge of the Volcano national park, Hutu extremists kept a low-level murderous insurgency going until late last year.
Now there are fields of white pyrethrum flowers, peasants hoeing potatoes, herds of cows, newly created villages of formerly displaced people. Ruhengeri is near the home area of Juvenal Habyarimana, who was president in the former Hutu-dominated government, and a centre of the authoritarian regime that organised the genocide campaign and urged people to join in as a duty.
Last month, in a school just outside the town, the government finished a 14-week political education course for 2,000 people, many of them its former opponents or returnees from the Congo.
'There has been a tremendous change here over the last four to five months,' said the army commander for the area, Lieutenant-Colonel Alex Kagame (no relation of Rwanda's vice-president, Paul Kagame). The change is recent enough, however, for United Nations personnel in the capital, Kigali, to still consider it unsafe for them to travel to the north- west.
The Tutsi-Hutu coexistence of 1994-96 collapsed in this area after the interahamwe's camps were dispersed in Congo, a former commander in the region, Brigadier-General Nyamwasa Kayumba, explained.
'Ideology came back, Tutsis were targeted, and the population were being mobilised to kill again. It was extremely difficult separating the insurgents from the population - they are relatives, friends. But then we started explaining to the people that they were losing in social and economic terms as the insurgents destroyed schools, hospitals.'
Gradually, he said, the weakened insurgents 'started to give themselves up'.
In the last few months the mood had changed, he said, with the realisation, that the balance of forces in the country had shifted decisively and the genocidaires had no chance of returning to power.
On the roads occasional groups of men in pink pyjamas appear on their way from jail to do agricultural work. They too have changed. There are still about 100,000 genocide suspects in prison, but since the execution of 20 killers last year, and the release of 10,000 prisoners, there have been many confessions and pleas for clemency.
Across the border from the villages, Rwandan troops now control the Masisi area of eastern Congo, which was a no-go area run by the interahamwe for nearly three years; that too is part of the changing dynamic.
'Two hundred or so have come back recently from Congo,' Col Kagame said. 'They come in groups of five, 20, 50, sneaking away from the interahamwe with their families, and going back into their own commune. Most of them are never arrested: the population must decide what these individuals did. For one to be denounced there must be many witnesses and a file prepared on them.'
The renaissance of Rwanda is a subtle process in which judgments about individuals' guilt are being made daily by survivors in countless villages where the terms of coexistence with the guilty of 1994 are worked out in practice. The role of outsiders continues to be overwhelmingly negative. The new threat to Rwanda from Congo and its allies, Zimbabwe and Angola, is being compounded by a persistent disinformation campaign on the Internet and in African diplomatic circles saying that Rwanda is linked with Jonas Savimbi's Unita rebel movement in Angola.
Equally damaging, and similarly part of a propaganda campaign with a long history, is the accusation by the US-based monitoring organisation Human Rights Watch that the government of Rwanda is responsible for a 'massive slaughter of civilians' in Congo and Rwanda.
Nevertheless, the report - an 80-page book by Alison Des Forges called Leave None to Tell the Story - will be important to a new study of responsibility for the atrocity which being undertaken by the UN at the request of its secretary-general, Kofi Annan, who was head of peacekeeping in 1994. It tells in more detail than previously revealed how the UN, US, French, and Belgian authorities received dozens of warnings in a period of months of what Rwanda's leaders were planning, but failed to act.
'The Americans were interested in saving money, the Belgians were interested in saving face, and the French were interested in saving their ally, the genocidal government,' Ms Des Forges writes.
