This paper gives insight on organization and efficiency of agricultural research in Bulgaria during the period after country’s accession to EU. The analysis is predominately based on the research carried out in the Agricultural Academy—the main institution responsible for the organization of agricultural research in the country. Our analysis has found out that some of the Academy institutes and stations manage significant land and other resources, but the material and technical endowments of the majority of them is outdated, while some have no “critical” mass of human, financial and material resources needed for carrying effective modern research. The number of researchers and experts employed in the Academy is constantly decreasing due to insufficient budget funding, regulatory constraints, restructuring and layoffs, lack of acceptable pay and working conditions, insufficiently qualified candidates in some areas, etc. Since country’s accession to the EU, there has been a significant reduction in the overall expenditure and budget subsidies for agrarian research institutes and centers. Despite multiple “reforms” of the agrarian research system, the country still does not have an effective structure for organization of R&D and public funding systems, coordination and evaluation of research, evaluation and stimulation of researchers and teams, and protection of intellectual agricultural property rights. The trends and problems in the development of agricultural research in universities and Bulgarian Academy of Sciences are similar to those in the Agricultural Academy. There is no aggregated information about the nature and volume of agricultural research conducted by the Bulgarian universities, institutes of the Bulgarian Academy of Sciences, and in the private sector which requires the collection of similar information in the future in order to improve analysis and management.