The article addresses the analysis of the universities’ key performance indicators which are used in monitoring conducted by the Ministry of Education and Science of the Russian Federation. The author makes an attempt to define monitoring indicators which give a better idea of the effectiveness of the university, and draws attention to other indicators that are indirectly or in no way connected with the effectiveness of the educational organization. Based on the results of the work, the author offers his own concept of evaluation of Russian universities, based on the target efficiency model. The author’s concept of evaluation suggests differentiation of universities into 3 types, depending on the number of scientific, international and educational activities. It is proposed to evaluate the university only by those indicators that are provided by its type. The disadvantage of this model can be the subjective approach of experts in choosing the significance of each sub-indicator. On the positive side of this concept is the availability of a differentiated approach to universities of various types as well as the selection of indicators whose values are more dependent on the activities of university management than in state monitoring.