The general focus of the thesis is the protection of human rights in Europe. Clashing over values and other obstacles are frequent challenges in the multicultural European environment. Maintaining the balance between the universality of human rights and different national laws is often at the core of such issues. The European Union and the Council of Europe are crucial in maintaining this balance since the Member States of both are signatories of the European Convention for the Protection of Human Rights and Fundamental Freedoms (ECHR). The main focus of the thesis is the challenge of securing freedom of thought, conscience and religion, according to article 9 of the ECHR, for the expression of religious convictions and practices of both Muslim and Christian faiths. The role of religion has changed greatly in the international environment and I am interested how the changing role of religion is reflected in Europe. The theoretical part of the thesis derives from the Multi-level governance theory, which tries to explain how these new systems of governing are developing in Europe, even in the functioning of European Courts. The empirical part is focused on six European Court of Human Rights (ECtHR) cases. The case analysis focuses primarily on the mechanisms used by the ECtHR in determining possible violations of Article 9 of the ECHR. The main goal of this thesis is to bring European law closer to the field of social sciences and to raise awareness on the functioning of the ECtHR and on the importance human rights.