This article analyses the situation in the sphere of science and higher education integration in the Republic of Moldova, produced within the international project FKTBUM "Fostering the knowledge triangle in Belarus, Ukraine and Moldova". The authors consider the main indicators that show the results of research activities at universities and their role in the transfer of the latest scientific achievements in the educational process. The authors attempt to rehabilitate Moldovan universities based on the capacity assessment of higher education institutions of the Republic of Moldova, undertaken by a committee of experts in 2014, which states that the national system of higher education in the Republic of Moldova is focused more on the educational component, considering research activities at universities as a minor component. It is proved that higher education institutions of the country, being a cradle of scientific staff, are so closely associated with science that it is incompetent to separate these phenomena. It is stated that the academic staff actively participates in scientific research and develops an excellent platform to promptly disseminate its results in the society. The comparative data provided in the article include a number of leading universities of the Republic of Moldova and reflect the extent of their participation in publishing and project activities, their role in the training of new scientists. The authors draw attention to the fact that funds for scientific research are distributed unequally, which is a constraint to the involvement of universities in research activities. Comparing investment activities in science in different countries, the level of university graduates' involvement in research activities, the authors arrive at a conclusion about the need to appeal to the European experience, where the involvement of scientific and teaching staff in research activities is encouraged and strongly supported by the state, private business structures and autonomous university policy, which becomes extremely important if we take into account that the Republic of Moldova has signed an Association Agreement with the European Union.