Multidisciplinary collaborations are increasingly predominant in innovative industries facing complex challenges. Yet, too frequently managers fail to identify the appropriate situations in which collaborations can be efficient, as their dynamics are not fully investigated. We examine multidisciplinary collaborations, their pertinent agents and complementary network capabilities in the context of the pharmaceutical industry. We focus on three research issues: a) how do multidisciplinary partnerships operate in the pharmaceutical industry? b) at what level are they most relevant (e.g. for knowledge external to the company, or internal)? c) what are the main challenges and benefits of multidisciplinary collaborations? We analysed empirical data from two different innovative pharmaceutical firms: a global top-ten corporation based in UK and an international firm located in a small/medium European economy. Our research is using a comparative case study design, drawing strongly from the literature. This research design provides a strong empirical grounding for a rich, in-depth, understanding of multidisciplinary collaborations in the pharmaceutical R&D process, with strong focus on the nature of internal and external partnerships and their impact in the organisation. The findings indicate that innovation management is increasingly reliant on multidisciplinary organisational arrangements; attention to complementary network and agent-related externalities has become vital for the success of the pharmaceutical company. Good managerial practice for multidisciplinary practice is more complex and nuanced than the literature may indicate and relies on flexible, adaptive and contextual processes.