While 2012 reportedly saw fewer killings than the preceding year, ongoing political violence between the dominant party, the National Council for the Defense of Democracy-Forces for the Defense of Democracy (CNDD-FDD) and opponents continued to threaten Burundi's stability. Widespread impunity remained a critical issue, especially concerning members of the security forces and persons affiliated with the youth league of the CNDD-FDD. And journalists and civil society organizations continued to feel pressure, with draft legislation curbing press freedoms being proposed in the Burundi parliament in October.

After Tanzania revoked their refugee status and announced plans to close their camp by the end of the year, more than 34,000 Burundese refugees returned home in late 2012. Upon arrival they faced a Ministry of Health-declared national disaster: a cholera outbreak, which was particularly severe in returnee areas.

The situation of Burundi's Batwa people was one focus of the Universal Periodic Review (UPR) of Burundi's compliance with human rights standards by the UN Human Rights Council in 2012. Burundi's report stressed that its Constitution mandates respect for ethnic diversity, that the rights of all citizens are protected equally, and that it was implementing non-discrimination measures in favour of Batwa children, for instance by funding their secondary education.

During the review a number of UN agencies expressed concern about discrimination against Batwa with regard to access to land, education and employment.

Further issues were raised during the UPR process. Several NGOs drew attention to the fact that poverty remained more prevalent among Batwa than among other groups.

Other issues of concern during the review included the level of malnutrition among Batwa children, their lack of access to full medical treatment due to their families' poverty, and the inability of Batwa women to access maternity care due to lack of identity documents.

For its part, the United Nations Integrated Management Team in Burundi (UNIMT) expressed concern that medicines for chronic illnesses were not affordable for Batwa, among others.With regard to MDG 4, on reducing child mortality, and MDG 5, on reducing maternal mortality, Burundi had by 2010 made some progress; however it reported that it was not likely to meet the 2015 targets. With regard to MDG 6 on reducing infectious diseases, it reported that stopping the spread of HIV was improbable, but achieving goals in reducing malaria and other infectious diseases, on the other hand, was possible.

One of UNAIDS' 22 priority countries, Burundi achieved a moderate decline in new HIV infections among children between 2009 and 2011 (MDG 6).

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