The main issue discussed in this paper is the question of characteristic features and main problems of the universal refugee law system based on the Geneva Convention relating to the Status of Refugee from 1951 with its 1967 Protocol applied in cases of fear of Female Genital Mutilation. Referring to the concept of positive obligations of states and its horizontal effect developed by European Court of Human Rights, the paper points out the difficulties of protection from FGM caused by its different socio-cultural and legal aspects. It examines theoretical and practical issues that raises during the process of interpretation and application of the Convention, it takes into consideration states' jurisprudence as well as influential work of United Nations High Commissioner for Refugees that helped to develop the good practice.