Although Indonesia has acceded to the International Covenant on Civil and Political Rights and freedom of religion is a mandate of the 1945 Constitution, there is a significant difference between the promise and the practice of religious liberty, especially regarding the rights of sects in Indonesia. The article explores this theme in the context of the Congregation of Ahmadiyah Indonesia, a minority Islamic sect which is not considered as an agama, or official religion, as a case study. This designation has had various discriminatory effects on its adherents, which waters down significantly the guarantee of religious freedom in Indonesia.