In the ascension of contemporary civilization a special role is given to universities. The mission of these institutions is formation through training, culture and research. The classical university was conceived as an institution that gathers people conducting scientific research and at the same time as an institution that form and educates specialists in various divisions of the economy and culture. Unlike the medieval universities, where persists the professional character of higher education, the modern university, inspired by the ideals of Enlightenment, becomes a research institution, alongside the academies, assuming both education and research.. This article aims to elucidate and argue the main stages in the evolution of the institutionalization of scientific research in universal university activity. Concerning the context of scientific research in the universities of the Republic of Moldova, the main restructurings in the 1990s of the 20th century, the state policy in the sphere of research and development in the years 2001-2017, the period when the coordination of the scientific research came back Academy of Sciences. The reasons for the academic scholars' disagreement over the unsatisfactory situation of university research and the merger of the Academy of Sciences with the Ministry of Education are also explained, phenomena that marked the beginning of a new period in the development of university science.