Ethnic minorities and women are politically under-represented in Tajikistan. There are no female or minority ministers; and out of the 96 seats in the upper and lower chambers of parliament, only two are occupied by ethnic minorities and 17 by women.

In May Salim Shamsiddinov, an Uzbek community leader in southern Tajikistan's Khatlon region, was seriously assaulted after he publicly claimed the government was pursuing nationalist policies. He has since gone missing in what Amnesty International suggest was a political abduction. Elsewhere in 2012, the US State Department reported occasional harassment of Afghans and Uzbeks by law enforcement officials.

In Tajikistan 7,500 children under the age of five die every year of undernourishment according to a 2012 report by the World Bank and UNICEF. A third of children have stunted growth and there is high prevalence of anaemia and other health impacts from lack of food, according to the report. This was found to be most prevalent in rural Khatlon, with a significant Uzbek population, and Gorno-Badakhshan Autonomous Province, where ethnic Pamiris mainly live. President Emomalii Rahmon's lack of connection with his people – especially minorities in these rural areas – was shown when he criticized his citizens' unhealthy eating habits and lack of exercise, which he thinks leads to high levels of obesity.

Violence erupted in Gorno-Badakhshan Autonomous Province in July, after a local state security official government official was murdered. The government sent 3,000 troops to the autonomous Pamiri region to arrest Tolib Ayombekov, an opposition leader from the 1990s Tajik civil war who was blamed for the assassination. The violence led to numerous deaths and injuries, including among civilians, according to HRW. A majority of the region's population belongs to the Ismaili sect of Islam; representatives of the movement's spiritual leader, the Aga Khan, were involved in negotiation efforts to diffuse the situation.

Tensions continued through August, however, as local Pamiris protested after the murder of another former opposition leader, Imomnazar Imomnazarov. The government conceded that they would withdraw at the end of August but sporadic killings and skirmishes continued into September.

The Tajik government further tightened restrictions on religious freedoms in 2012, introducing new penalties for those receiving religious education abroad, preaching and teaching religious doctrines, and establishing connections with foreign religious organizations. This move led to Tajikistan joining Turkmenistan and Uzbekistan as a 'country of particular concern', according to the USCIRF 2013 report.

The report notes that restrictions and abuses primarily affect the majority Muslim population, but also Seventh-day Adventists, Baptists, Baha'is, Protestants, Jehovah's Witnesses and Hare Krishnas.

A repressive 2009 Religion Law prohibits all religious activity independent of state control. Those who participate in unregistered religious activity face up to two years' imprisonment. The 2011 Parental Responsibility Law stipulates that parents must prevent their children from participating in religious activity, outside state-approved religious education.

According to the Tajik State Department, as mentioned in the USCIRF 2012 report, only 74 of the 4,000 registered religious are non-Muslim, including Ismaili groups. Minority Muslim groups continue to face persecution; the Islamic Renaissance Party claims that numerous unregistered mosques have been demolished; the Salafi Muslim group has been banned since 2009; and in February it was reported that in December 2011 a mosque was raided for observing a Shi'a Muslim holiday when only Hanafi Sunni rituals should be observed. Muslim women are particularly repressed since a fatwa or religious decree issued in 2004 banning women from praying in Tajik mosques remains in effect. Women are also banned from wearing the hijab in schools and government offices.

In 2012, the Tajik government arrested citizens for belonging to alleged extremist groups such as Hizb-ut-Tahrir and Jamaat-i Tabligh (Society for Spreading the Faith), which has been banned since 2006. Members dispute claims that these groups have connections to terrorism and say they belong to peaceful organizations. In May, several alleged members of the Islamic Movement of Uzbekistan were arrested and tried behind closed doors.

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