We examine how R&D portfolios of drug pipelines affect pharmaceutical licensing, controlling firm size, diversity, and competitors in R&D and product markets. The data collected comprises 329 license-outs and 434 license-ins closed by 54 Japanese pharmaceutical companies between 1997 and 2007. We pay special attention to stage-specific licensing by dividing the innovation process into an early stage and a late stage. Estimates from the fixed-effect GMM model reveal that drug pipelines significantly affect stage-specific licensing. Particularly, the state of drug pipelines is leveled off by license-outs at the early stage and license-ins at the late stage. Theoretical implications are also discussed.