The issue of joint implementation of procedures for state, professional and public accreditation and certification of qualifications in the system of assessing the quality of higher education in Russia is considered in the article. State and public accreditation of universities exists in most countries of the world, based on it international ratings of efficiency and prestige of educational institutions are built. Certification of professional competencies is not a new phenomenon, but as a tool for assessing the quality of higher education, it takes into account not only the result of formal (state-system) training, but also parallel informal and spontaneous, which are not taken into account in the framework of state accreditation. In conclusion justified accreditation of higher education institutions, together with the certification of qualifications.