Corruption in healthcare generally and specifically in the pharmaceutical arena has recently been highlighted in reports by Transparency International. This article focuses on four areas of corruption: legislative/regulatory, financial, ideological/ethical, and communications. The problems identified and the solutions considered focus on structural considerations affecting how pharmaceuticals are discovered, developed, distributed, and ultimately used in clinical settings. These include recourse to user fees in the regulatory sphere, application of intellectual property rights to medical contexts (patents and access to research data), commercial sponsorship of ghost writing and guest authors, linkage/delinkage of the funding of research and overall health objectives to/from drug pricing and sales, transparency of payments to healthcare professionals and institutions, and credible regulatory sanctions. In general, financial and other incentives for all actors in the system should be structured to align with desired social outcomes - and to minimise conflicts of interest among researchers and clinicians.