Minorities have left Uzbekistan in very large numbers, partly as a consequence of the repressive regime of President Islam Karimov, but also because of the limited opportunities for minorities that are linked to discriminatory practices by authorities in favour of the Uzbek majority (US State Department, Country Report on Human Rights Practices 2004: Uzbekistan). The Russian-speaking minority has seen an exodus of almost a third of its numbers since independence in 1991, and in 2004 constituted only about 5 per cent of the population. The largest single minority, the Tajiks, probably comprise close to 8 per cent of the population, but they remain largely excluded in many areas of public life. The regime of President Karimov has often been seen to target Tajiks. Thousands of individuals are detained for political or religious reasons, including human rights activists. The position of minorities in the country is thus similar to that of others who experience the difficulties of living in a repressive regime. The Russian language is still widely used by state authorities in daily activities, however, despite the Uzbek language being the only official language. The fight against terror and fundamentalism has in Uzbekistan an ethnic dimension which has severely impacted on the Tajik minority, with the forcible resettlement in 2000 of thousands of mostly ethnic Tajik families from southern mountain villages, burning and bombing of mainly Tajik villages, and the destruction of their homes and fields because of allegations that Islamic militants had infiltrated these villages.

Because of a special autonomy arrangement granted to the Republic of Karakalpakstan, the Turkic-speaking Karakalpaks have in legal and practical terms much greater protection of their rights and in the use of their language, though they comprise less than 2 per cent of the population. The status of other minorities, and the use of their languages, are significantly less, and in the case of Tajik almost non-existent outside of some localities despite their being present in greater numbers than Russians.

The repressive regime took a particularly bloody turn in 2005 following the Andijan massacre. Hundreds of unarmed people protesting in the eastern city of Andijan, perhaps as many as 750, were killed on 13 May 2005 by Uzbek government forces. The protest started when a group of armed people freed a group of 23 local businessmen accused of Islamic extremism and took officials hostage in the local government building. The protest then grew into a rally of thousands of mostly unarmed people who voiced their anger against government corruption, repression and growing poverty in the region.

The massacre led to widespread condemnations – including European Union sanctions in 2005 – though these still seem surprisingly muted given the massive numbers of unarmed civilians, including women and children, who were killed by security forces. The US was 'ejected' from Uzbekistan for its criticisms when the Uzbek government requested it leave its military base in southern Uzbekistan. Russia has been supportive of President Karimov's actions and indeed increased its presence and conducted joint military exercises with the Uzbek military in September 2005.

Overall, the situation of minorities has seen no improvement in 2004–5. For religious minorities, reports following the Andijan massacre suggest there is in fact a tightening of that country's repressive religion policy. In addition to members of the Tajik minority who may be tagged as 'fundamentalists', religious minorities such as Hare Krishna, Jehovah's Witnesses and Protestants in Karakalpakstan (where all activities of this minority have been banned) show an increase in 2005 in restrictions and prohibitions. Indeed, the repressive nature of the government restrictions on religious activities, including from non-government-sanctioned Islamic groupings, may breed further resistance in the next few years.

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