Examined is relevance of a subject of work is caused by the continuing deterioration of dissertation works. Therefore, article purpose is to define the system reason of deterioration of training of the top skills by the analysis of contents and structure of theses. The main shortcomings of dissertations, and understanding of their structural elements by applicants of an academic degree by communication with them in the course of preparation and carrying out preliminary protection of these were analyzed. Results of the analysis were compared to requirements of classical methodology and to interpretation of these requirements in the methodical managements and in publications. The essential system reason of decline in quality of dissertation works is in their traditional unsystematic structure, whith investigation withdrawal from scientific methodology and particular leveling of motivation to the analysis of a condition of a question and the received results of researches and also to system approach to the thesis, need of strengthening of methodological training of graduate students according to the uniform nation-wide program providing system approach to the organization of researches for all scientific specialties, and processing’s of the “Thesis and Abstract of the Thesis” standard according to classical requirements of scientific methodology and the system approach to dissertation work Is shown. The system scheme of the thesis, which can make a manual basis is the practical guide to organization and performance of dissertation work for training of graduate students and applicants is offered.