The aim of the article is to present and use the methodology for the assessment of the functioning of higher education institutions. The article uses the proposed methodology to assess the efficiency and quality of leading public higher education institutions operating in Poland. The basis of the proposed methodology is, on the one hand, the observation that the higher education institutions implements two main processes (significantly differing in the nature of expenditures and the obtained products and outcomes) didactics and research. On the other hand, in order to obtain a comprehensive higher education institutions assessment, it is important to address two areas: the efficiency of functioning and the generated quality (understood as the impact of the higher education institution on the environment). The research results indicate that both in the case of didactics and research, the highest level of efficiency was recorded in the case of the University of Warsaw. The presented results indicated the possibilities offered by the proposed methodology, however, reflection on the selection and sources of the analyzed data is important.