Technological innovation is represented by the conversion of knowledge into new products and processes which, when commercialized, generate wealth. In relations with companies, universities’ role is to develop scientific knowledge, fostering industry’s R&D activities. This article proposes an analysis of the technology transfer process performed by public universities in Brazil. Results demonstrate that universities are facing difficulties in requesting and licensing patents based on scientific results, due to lack of commercial contact with companies and their limitations in adapting available technologies. The increase in scientific output is not being effectively transformed into new technologies for products and services, exposing the necessity for new policies to approach university-industry relations. For universities, this may mean rethinking the role of patents in the technology transfer process, such as increasing co-authorship with companies and have companies support technological research within the university, instead of investing in legal protection, distant from market needs.