Greece has been an EU member state since 1981, but has not ratified the FCNM and does not recognize the existence of ethnic minorities on its territory. Only a 'Muslim minority' in Western Thrace, protected by the terms of the 1923 Treaty of Lausanne concluded with Turkey is officially recognized as a religious minority, but its predominantly ethnic Turkish members are denied recognition as an ethnic minority. The non-recognition of the ethnic Turkish and Macedonian minorities has profound ramifications for the ability of these minority communities to exercise their rights. The persistent refusal of Greek courts to register minority associations has constituted a violation of their right to freedom of association, as the ECtHR has found in four separate cases – to no avail, as the courts still refuse to grant registration to all of them. It has also been detrimental to the protection of minority identities, making it impossible to institute adequate arrangements in areas such as minority language use or education.

The state of minorities in Greece prompted both the High Commissioner for Human Rights of the Council of Europe and the IEMI to undertake country visits in 2008. The High Commissioner was primarily concerned with minorities and the right to freedom of association, the denial of citizenship to some members of minorities under former legislation, and issues affecting the religious freedom in particular of the Turks in Western Thrace as government-appointed Muftis have been reported to apply Sharia law in family and inheritance matters, in contravention of international human rights standards. The IEMI raised a variety of issues, including the protection of minority identity, minority religions and discrimination against the Roma in housing and employment, education and denial of justice.

However, the Greek state reaffirmed its position that 'any recommendation by UN treaty bodies and by other monitoring mechanisms, on the protection of rights of persons claiming to belong to a minority cannot determine the existence of a minority group or impose on States an obligation to officially recognize a group as a minority', as articulated in the government's reply to the report of the High Commissioner for Human Rights. There was a similar reaction to the report of the IEMI.

The National Commission for Human Rights (NCHR) reviewed the results of the implementation of the 'Integrated Action Plan for the Social Integration of Greek Gypsies 2002-2008'. The report, co-signed by the Deputy Ombudsman for Human Rights, assessed the housing initiatives as 'rather modest'. It emphasized the negative attitude of local authorities and communities towards such programmes: 'The municipalities are very reluctant to attempt any form of registering the Roma residing in and/or passing through their areas; they invoke the fact that any record based on "racial" criteria is prohibited by law', the report stated. The NCHR and the Deputy Ombudsman urged the Greek state to change the way it responds to the recommendations of domestic and international bodies dealing with Roma. 'Execution of the judgments of the European Court for Human Rights and compliance with the observations of other jurisdictional organs,' they stressed, 'is an obligation and not an option.'

Finally, concerning minority religions, the IEMI noted the considerable influence of the Greek Orthodox Church in Greek society and political life, and that the Church receives state funding; that there is no specific domestic law to protect freedom of religion; and that members of other religions face verbal and sometimes physical aggression, as well as restrictions on places of worship and burial sites. In addition, in 2008, the ECtHR in the Alexandridis v. Greece judgment ruled that the fact that the applicant had had to reveal that he was not an Orthodox Christian while taking an oath of office before a Greek court in order to take a non-religious affirmation had interfered with his freedom not to have to manifest his religious beliefs and therefore constituted a violation of Article 9 of the European Convention.

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