In response to the increasing number and breadth of innovation studies on the pharmaceutical industry, we mapped the literature to show the trends in recent research and to indicate areas for further research. In the first phase, we analyzed articles on the pharmaceutical industry published in innovation journals. We used these articles’ textual and citation data and applied hybrid cluster analysis. Three main clusters were produced based on the level of analysis innovation scholars had used to investigate the industry: macro, meso and micro. We describe the research topics within these clusters and show that, overall, innovation scholars increasingly focus on the meso-level, analyzing the relationships across different firms. This shift in interest toward the collaborative nature of drug discovery and development was also apparent in macro- and micro-level studies. To explore how this literature is used by scientists in the industry, our second phase involved analysis of the citing articles published in pharmaceutical journals. Using our findings, we propose research areas that can be further explored in order to create an engaged and better-integrated literature on pharmaceutical innovation.