Abstract: The subject of this research is the key capabilities and competencies of the higher education institutions that are formed by the modern reform in the system of education within the Russian universities and the leading world educational establishments that achieved significant success. The authors carefully examine such aspects of the topic as the analysis of processes of development of capabilities and key competencies in Russian universities within the framework of the three directions of the work of educational establishment: scientific, educational, and innovational. Special attention is given to the analysis of gaps and realization of benchmarking of the educational processes and results of a university. During the course of this work, the authors determine the key controversies in the process of bencharking within the Russian educational environment: orientation of capabilities and competencies of the Russian higher education institution not towards their advancement or highly competitive market of education services, but rather satisfaction of the interests of central office; lack of strategic orientation of a number of forming competencies and capabilities; orientation towards operating activity, etc. The conclusion is made that at the present stage, the reforms in higher school do not provide the formation of capabilities and “key competencies” of the Russian higher education institutions, which will allow increasing their competitiveness on the global arena, meet the demands of the real sector of the economy, as well as efficiently realize the initiatives on innovation development.