As universities around the world are under pressure to produce commercial outputs of their research results, it is surprising how a few studies have been conducted about intermediary organizations and their role in this matter. The intermediaries’ basic roles to diminish market and system failures in innovation processes are targeted to respond to the challenges that may emerge in innovation processes, in general, especially in the commercialization of academic research. In this article, we analyse the roles of, and needs for, different kinds of intermediary organizations in two Finnish technology agglomerations from the perspective of the commercialization of new knowledge. We use the Triple Helix concept as a theoretical starting point for our empirical analysis. As many challenges in Triple Helix linkages prove that policy interventions to support the activities of intermediary organizations are justified up to certain point. However, the role of these “go-between” actors may also be irrelevant if networks between university–firm–government helices function well. In addition, many of the challenges in the commercialization of new knowledge originated from the failures of policy implementation concerning the public or semi-public intermediaries.