Economic partnerships between industry and academia accelerate medical innovation and enhance patient access to medical advances, but such partnerships have sometimes eroded public trust in the research enterprise. There is particular risk for conflict of interest when economic partnerships extend beyond a university's corporate interests to involve institutional decision makers. Institutions and institutional decision makers should fully disclose industry-related financial interests and relationships. Without legitimate justification for such interests, individuals should divest themselves from these interests or recuse themselves from responsibility for research oversight. Management of institutional partnerships also might entail the physical separation of certain facilities, the placement of restrictions on information shared between investment and research staffs, and provision of oversight by independent review panels made up of persons who have expertise in intellectual property, finance, and research, but who are not financially or otherwise dependent on the institution. Through these means, it is possible to restore balance to industry-academia relationships, thereby promoting progress while maintaining public trust in research.