In response to the violence in Kyrgyzstan, Uzbekistan's President Karimov repeatedly stated that the conflict was not inter-ethnic, and stressed the importance of inter-ethnic unity. State television followed suit, carrying many programmes emphasizing inter-ethnic harmony in the country. However, local observers state that this campaign does not address structural discrimination, especially the issue of Uzbek nationalism and the exclusion of ethnic minorities from public life.

Uzbekistan allowed up to 100,000 refugees from Kyrgyzstan, the vast majority women and children, into the country in mid-June. Large refugee camps were established by the authorities, who requested international support. However, within two weeks, at the request of Kyrgyzstan's interim government, almost all were returned. Reports indicate that some were forced to return, in clear violation of the widely held international legal principle of non-refoulement, namely that no one should be returned to situations where their life or freedom is threatened. There were reports in December that several thousand ethnic Uzbeks from Kyrgyzstan remained illegally in Uzbekistan in December, but that many of them were seeking to leave for Russia or Western Europe for fear of deportation and lack of financial means.

Uzbekistan's ethnic Kyrgyz minority, which is primarily concentrated in Andijan, Fergana and Namangan provinces, remained fearful of potential reprisal attacks. There has reportedly been a sharp rise in hostility towards Kyrgyz in Uzbekistan, partially reflected by a prominent singer recording a song entitled 'To the Kyrgyz' about the inter-ethnic violence. Since the June events, there has been an increased security presence around Kyrgyz villages, ostensibly to protect villagers from potential attacks by Uzbek vigilantes.

The autonomous republic of Karakalpakstan makes up a third of the area of Uzbekistan (in the east), and has large reserves of oil, gas, titanium and gold. It surrounds the remnants of the Aral Sea, devastated by decades of overproduction of cotton in Central Asia. Sixty per cent of its population are ethnic Karakalpaks and Kazakhs, and there is apparently a separatist movement that would like the republic either to become part of Kazakhstan or secure full independence. Reportedly, tens of thousands of people have left Karakalpakstan for Kazakhstan in recent years, despite government measures to prevent this, including a ban on the sale of housing. This is partly connected to Kazakhstan's continued promotion of immigration of ethnic Kazakhs to the country. Recently, there have been reports of a rise in anger at perceived injustice against the people of Karakalpakstan. In November, the sale of equipment from an animal feed-producing plant in the town of Chimbay in Karakalpakstan to neighbouring Khorezm province by Uzbekistan's State Property Commission led to an angry anti-Uzbek demonstration in the town, which was broken up by riot police.

After a visit by the OSCE's High Commissioner for National Minorities in early April, Uzbekistan's government showed its defiance by cracking down on minority representation. In April, the Kazakh Cultural Centre in Nukus, Karakalpakstan's capital, was given one month to address alleged legal violations or face closure. Meanwhile, the head of the Jewish Cultural Centre in Tashkent was refused an extension to his accreditation in April after legal violations were also allegedly found there.

Uzbekistan has continued to tighten its borders with neighbouring countries, and this has affected local residents in border areas who are often from minority ethnic groups. In July, it was reported that 42 houses were to be demolished in a primarily ethnic Kazakh border village in Tashkent province. No government order was shared with residents, and it was unclear if compensation was to be paid. In September, the disputed village of Chek on the border with Kyrgyzstan was formally annexed by Uzbekistan. Twenty-four families who wanted to remain citizens of Kyrgyzstan (of whom 20 were ethnic Uzbeks and four Kyrgyz) had to relocate to another village inside Kyrgyzstan.

Tajiks, who are prevalent in and around the cities of Bukhara and Samarkand, have reported discriminatory government policies. There are reports that Bukhara city authorities recently closed Tajik-language schools. And the city administration in Samarkand is reported to have sacked Tajiks from the bureaucracy in 2009. Simmering Uzbek-Tajik tensions reportedly fuelled small-scale incidents in Risthan, a small town in the Ferghana Valley, as well as in Samarkand and Bukhara, according to local observers. The authorities reportedly suppressed media coverage of these episodes. Meanwhile, Samarkand has been undergoing renovation. According to an opposition website, approximately 100 private residences and 30 businesses were demolished between October 2009 and May 2010, despite protests by their owners. Citing residents, the report claimed that officials gave residents only three days to vacate their properties. Many of those who lost their homes are now reportedly staying with relatives, or living in rental housing. Government promises of compensation have not been kept.

Discrimination against religious minorities is also common in Uzbekistan. Forum 18 reported that in 2010 short-term sentences were reinstated for members of religious minorities for organizing or taking part in unauthorized religious meetings or otherwise expressing their religious beliefs. Some Protestants and Jehovah's Witnesses were sentenced to 10- and 15-day prison terms, while a Baptist who had been sentenced to ten years' imprisonment lost his appeal. In April, three Muslim women were sentenced to between six and a half and seven years in a labour camp for leading and taking part in illegal religious meetings. Furthermore, female members of these religious groups have reportedly been threatened with sexual violence and torture by the police while in detention for practising their religion.

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