The article reviewes changes in the Russian higher education in the last decades. Among innovations with impact on functioning of higher educational the transition to a twolevel system of education, creation of federal and national research universities, changes in payment of teachers etc. are noted. Severe social and economic conditions are have increased the role and complicated the work the heads of University departments setting new priorities to their activities and professional competence. The article presents results of the monitoring of changes in the staff and the content of the activity to the Department heads. At the beginning of the 2012/2013 academic year the average age of the heads of departments exceeded 54 years, – considerably higher than in 2002. To improve the professionalism of the heads of higher educational institutions (rectors, deans of faculties, heads of departments) a set of studies was conducted – “Management in education”, “Management of department”, “Management of faculty”, “Management of the higher educational institution” and others. In the conclusion of the article, the authors justify the need for new monitoring of activities of the heads of Russian universities departments, which will allow to identify new reserves for improving their activity, to identify key areas that should be given special attention to in the educational process, scientific research and educational work.