The government increased several tax rates in 2001 in an attempt to meet the target of increasing its tax burden (at about 10.7% of GDP, currently the lowest in the region) to 12% of GDP. However, protestors took to the streets massively when the government sought further increases in August 2001, declaring their opposition to any new taxes until the Portillo administration provided better accountability for the taxes it already received.

Violent harassment of human rights workers presented a serious challenge in 2002 and 2003. Common crime, aggravated by a legacy of violence and vigilante justice, presented another serious challenge. Impunity remained a major problem, primarily because democratic institutions, including those responsible for the administration of justice, have developed only a limited capacity to cope with this legacy. Guatemala's judiciary is independent; however, it suffered during 2003 from inefficiency, corruption, and intimidation.

In early 2003, the government accepted the Human Rights Ombudsman's proposal for a U.N.-led commission to investigate possible links between illegal clandestine groups or security forces and attacks on human rights defenders and organized crime. By the end of 2003, the agreement was scheduled to be submitted to the Congress for ratification in January 2004. The UN Verification Mission in Guatemala (MINUGUA) ceased its 10-year project of monitoring peace accord implementation and human rights problems in November 2004 with UN Secretary General Kofi Annan declaring Guatemala had made ìenormous progress in managing the countryís problems through dialogue and institutionsî. The United Nations and Guatemala agreed to open an Office of the High Commissioner for Human Rights and form a special body to investigate clandestine groups. That operation began in January 2005.