Discussions concerning the position of Muslims in the Netherlands featured prominently in the public debate on discrimination and racism during 2009. Islam is frequently portrayed as a threat to Dutch society by politicians and public figures. After the far-right Freedom Party leader Geert Wilders made a controversial film equating Islam with violence and the Qur'an with fascist texts, an Amsterdam court ordered prosecutors to put him on trial. The decision followed numerous complaints by human rights groups and citizens over the prosecution services' refusal to press charges against Wilders, and stated that, 'in a democratic system, hate speech is considered so serious that it is in the general interest to ... draw a clear line'. The court order is notable, as Dutch courts tend to be reluctant to restrict freedom of expression when it concerns statements made by politicians and public figures. Wilders attracted headlines in the UK during 2009, when he was stopped from entering the country. He had been invited by the Eurosceptic UKIP to screen his film, but the then Home Secretary Jacqui Smith banned his entry. The ban was later overturned by a High Court decision, leading to Wilders' visiting the UK in March 2010. He screened the film at the House of Lords, upon UKIP's invitation.

Muslims constitute around 5.2 per cent of the population and are mainly concentrated in larger cities. According to 2008 figures of the Central Bureau of Statistics, there are approximately 373,000 Turks and 335,000 Moroccans; other Muslims come from the country's former colony of Suriname or are asylum-seekers from the Middle East. As the 2009 report of the US Commission on International Religious Freedom (USCIRF 2009) notes, the Turkish government appoints imams for most of the more than 200 Turkish mosques in the Netherlands. The Dutch government provides funding for education in religious schools and other religious institutions. Headscarves are in practice permitted almost everywhere, including in schools. A ban on face-covering religious clothing was however introduced for teachers, parents and students in educational settings, and also for government officials interacting with the general public. In May 2009, a court ruling also introduced the requirement that female school staff shake hands with males in greeting, even if this goes against their religious affiliation.

While a government report released in 2009 shows that integration of ethnic and religious minorities has improved in the last couple of years, human rights groups and the CoE indicated otherwise. Human rights group Defence for Children International warned that the rights of migrant and refugee children are inadequately guaranteed in the Netherlands, and that those separated from their parents are vulnerable to abuse or ill-informed about their rights.

CoE Commissioner for Human Rights, Thomas Hammarberg, also emphasized that 'policies towards migrants and asylum-seekers require further review' in the country report presented in March 2009. Addressing issues concerning discrimination and intolerance, the rights of the child, anti-terrorism measures and ethnic profiling, the Commissioner recommended that the protection of minority rights be strengthened.

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