The present paper is aimed at highlighting the changing pathways of the knowledge production process in the Higher Education and University System. Particularly, special attention is given to the impact of historical turning points in our society, like the World War II, the capitalism, and the advent of globalization, on the re-organization of the University and research institutes according to the criteria and mechanisms of the market. Alongside the spreading of mass higher education, the issue of how defining excellence, relevance, and quality of research and teaching activities arise, as well as the issue of ranking scientific works, researchers, and journals. This has forced the introduction of quantitative indicators to evaluate the big amount of research outputs and, in parallel, fostered the creation of quality hierarchies to better orient experts in the research field. This revolutionary change of paradigm was supported by the loss of trust in the process of peer-review that paved the way for the emergence of the need of having alternative parameters to rank the scientific work of a researcher. The pro and cons of bibliometric indexes and peer-review procedures are discussed.