Universities’ centrality within the public research systems has been increasing over time, as it has their interactions with industry. Such interaction poses two dilemmas. One concerns individual scientists and the potential trade-off between basic research activities and those activities required to successfully develop and commercialize academic inventions. The second dilemma occurs at the system level, and it has to do with the tension between the industry’s need to rely upon clear and solid intellectual property rights (IPRs), and the cumulativeness of the scientific enterprise, which requires the results of academic research to be freely accessible. The empirical literature suggests that the first dilemma may not be as dramatic as expected by many. On the contrary, some evidence exists on the relevance of the second dilemma: commercial interests may exacerbate common threats to the commonality of research efforts; and the existence of IPRs over academic research results may discourage some scientists to build upon those results in order to advance knowledge. Existing bridging institutions, both internal and external to universities, seem to give only marginal contributions to the solution of both dilemmas.