The article is mainly devoted to the problems of teaching of Medical computer science in conditions of modernization in the education field. The modernization of education has demanded to design national educational standard. However, the attempts of its introduction have not brought desirable results yet. The authors consider that positive experience of Russian pedagogical science in the field of preparation high quality specialists, including Medical computer science, should be taken into account in the situation of modernization educational system. The article provides a comparative analysis of training course «Medical Informatics» in the Russian and European universities (for example, Germany), and describes the experience of the implementation of new approaches to teaching students in accordance with the requirements of the GEF and the problems encountered in their implementation at the Department of physics and Informatics of Altai State medical University.