There has been little consensus between the pharmaceutical industry and academic communities concerning the best approach to train medicinal chemists for drug discovery. For decades the pharmaceutical industry has shown preference for synthetic organic graduates over candidates with degrees from medicinal chemistry programs on the assumption that medicinal chemistry expertise will be acquired on the job. However, ongoing changes to pharmaceutical drug discovery organizations and practices threaten to undermine this training model. There is a compelling argument to be made for establishment of a strong industry-academic partnership to train new candidates with sophisticated knowledge of contemporary drug design concepts and techniques to ensure that the future needs of both industry and academic drug discovery research can be served.