A vital aspect of the Church of Sweden is its Lutheran confession and its emphasis on the Two regiments doctrine - an equal interest of working together in the Nation state of Sweden. According to Casanova (2014), the Nordic countries have experienced a secularism where religion has merged with the state and become a department. At the end of the 20th century, state and church separated, and the Church of Sweden became a "free" denomination. in the public schools, this separation has led to a conflict between the church and state. Thus, the distribution of rights according to the Lutheran doctrine is no longer valid. The state discards the Church of Sweden's "spiritual regiment" for the society, considering its religious practices as illegal within the school system. Ecclesiastical debates have begun on a new Lutheran identity formation within the church - that of a church of a minority in a postsecular context. The aim of this paper is to examine this identity formation and, the conflict over religious practices in the schools. New results from the research project "End of term ceremonies held in churches and the debate on the role of religion in Swedish schools", will be presented.