The aim of this paper is to describe the indicators for measuring different types of collaboration activities between universities and industry. Popular indicators for measuring university-industry cooperation are the number and amount of patents or licences, but these do not express the knowledge transfer and university-industry cooperation most adequately, as the collaboration and knowledge transfer also takes place through other types of cooperation. Although it is easier use input and output indicators for measuring university-industry cooperation, the focus should be on the economic impact of the collaboration. Additionally, relationship-based indicators should also be used. In Estonia different input factors are widely used. As university-industry cooperation is an input in innovation processes, the desired outcome should be a higher level of innovation, productivity, competitiveness, and growth, which has to be considered in the development of policies.