In April 2009, a Peruvian court made history as former President Fujimori became the first Head of State to be extradited back to his home country, tried, and convicted of crimes against humanity. He was sentenced to 25 years' imprisonment for his involvement with 'Grupo Colina', the paramilitary death squad responsible for executions and disappearances in the early 1990s. He was sentenced to a further seven years and six months for embezzlement of state funds. Although this landmark case marked a victory for human rights, most actors responsible for violations committed during the period of civil unrest continue to evade justice and the culture of impunity and the climate of threats to human rights defenders continue to exist.

Human rights defenders in Peru suffer from threats, intimidation, physical violence, criminal investigations and defamation. Thorough and independent investigations into these threats are rarely initiated by the relevant authorities. Members of the government sympathetic to former president Fujimori have sought to discredit those working to end impunity, and members of NGOs who advocate for accountability have also been accused of having links with terrorist groups, and of undermining military morale. The former president of the Truth and Reconciliation Commission himself has been the subject of death threats. Impunity for crimes committed by the authorities during the period of internal conflict remains an institutional problem, and at the end of 2008 two new bills proposing amnesties for members of the police and military implicated in violations were presented to Congress.

Journalists and broadcasters face threats and intimidation, particularly if they are seen to be working to uncover corruption or abuses by local government officials. Activists working in the area of social, economic and cultural rights have come under threat, including trade unionists and minority rights activists. Environmental activists and those defending the land rights of minority groups suffer threats and intimidation from state and non-state actors, agents who reportedly have vested economic interests in the exploitation of Peru's natural resources.

An NGO Bill that would have placed NGOs under closer state scrutiny and restricted freedom of association and expression was ruled unconstitutional in 2007. Despite this, a congressional committee has taken steps to reinstate the law, posing a very real threat to the work of human rights organisations.