In this thesis it is argued that while the concept of freedom of religion or belief itself is opaque and difficult to define, the right to religious freedom must contain certain basic factors – most importantly the right to individual (religious) autonomy. The individual autonomy approach is seen here as providing the necessary rationale for the protection of freedom of religion or belief. This rationale is not cemented in stone in the practice of the Convention and this has caused the Court to lose its focus on individual freedom. It is a dangerous tendency. It allows the focus to be placed on the role of the State and leaves freedom of religion or belief to be heavily affected by politics and fluctuating social attitudes. In this regard, this thesis looks for the meaning and scope of individual and collective religious autonomy and how it is and ought to be represented in the practice of the European Court of Human Rights. It is the aim of the author to contribute to a clearer and more principled understanding of Article 9 of the ECHR. The right to individual autonomy is thought to be able to provide the necessary focus for the European Court of Human Rights in creating a more robust framework for the protection of freedom of religion or belief different from current Court practice which shows inconsistency in its reasoning and theoretical chaos. This lack of clarity has also contributed to freedom of religion or belief being a relatively weak right. It is explored here as to how the principle of autonomy (as developed in this thesis) relates to other principles provided by the Court, namely the principle of State neutrality, pluralism and the effective protection of rights, but also the margin of appreciation and the autonomy of religious communities. The individual autonomy centred theoretical framework in the first part of the thesis will be engaged to analyse the conflict in the triangle of state-individual-community explored in the second part.