Subject. The article discusses the creation of innovative universities. Objectives. The purpose is to analyze the internal environment in the formation of an innovative university and to investigate the factors of resistance to organizational changes. Methods. The survey was attended by scientific and pedagogical staff of two innovative universities: 170 people from the Institute of Economics and Entrepreneurship of the National Research Lobachevsky State University of Nizhny Novgorod and 50 people. from the economics faculties of the Nizhny Novgorod Branch of the Higher School of Economics. Results. We analyzed internal environment and studied organizational changes aimed at creating new social mechanisms and channels of interaction with the State, industry and society. Furthermore, we considered the factor of resistance to organizational changes and the possibility of its reduction. The paper presents the results of diagnostics of the resistance force in two universities. Conclusions. The leading organizational factor (prerequisite) for the emergence of resistance is an imperfect system of organizational communications. The priority task of university management is to create an operational and objective system for informing employees about the goals, methods and results of changes. The most significant psychological reasons for the emergence of resistance are the fear of negative consequences of changes and misalignment of changes with traditional academic values.