This thesis addresses a topical issue of management of the antitrust-patent intersection, looking at the problem from an innovation perspective. It contributes to the field, first, by showing that from the innovation perspective the problem of biases present in both antitrust and patent decision-making might be a matter of concern in managing the antitrust-patent intersection. The question of pro-competition bias is explored through an analysis of novel issues recently considered by antitrust authorities. The analysed case studies concern reverse payment settlements, abuse of the patent system, availability of injunctions in the standard essential patent context and the treatment of the antitrust-patent intersection in the pharmaceutical sector inquiry Report prepared by the Commission. The corresponding risk of a pro-patent bias, already visible in the case studies, is examined in detail through an analysis of the design of the forthcoming Unitary Patent Court. Second, this thesis offers an examination of a signalling mechanism as a way of addressing the problem of biases. While observing that antitrust cases picked up by the Commission might serve as a signalling device for the patent system intended to prompt an alternative solution to the problem at hand, ways of developing further a communication by signalling outside the realm of enforcement are explored in an attempt to combat the risk of biases and to ensure an effective division of tasks. By adapting a signalling approach this thesis advocates an interdisciplinary approach to antitrust-patent intersection. It also seeks to combine the economic and a regulatory aspect of the treatment of the antitrust-patent intersection, thus giving it an EU-specific angle. The signalling justification for antitrust involvement in patent matters is based on the perception of the inadequacies of the alternative solutions as offered by the patent system, making an antitrust response grounded in the underlying regulatory system.