The shrinking economy has driven many investigators to seek industrial funding for both clinical and bench research. This has resulted in four concerns for the clinician scientist: (1) research that results in eff ective clinical application; (2) research design that meets evidence medicine requirements and has clinical signifi cance; (3) adherence to clinical competencies; and (4) research records that are open and refl ect both the scientific and economic path to the results of the investigation. This paper reports on how one institution protects the interests of all four stakeholders in any research study in academic centers: the investigator, the institution, patients, and industry. The process makes it possible for the investigator to concentrate on research methodology and to remain secure about the ethical conduct of their research. At our institution, all industrial-funded research is arranged on an institution-to-sponsor basis. Contract language is generated by the institution, not the investigator. This protects the investigator and includes freedom to publish regardless of the results. Issues of intellectual property, patient protection, and the institution's needs, such as intellectual property and compliance with the federal/state guidelines, and indemnification are incorporated into the pre- and post-award applications. Concurrently, Institutional Review Board (IRB) proposals are prepared and submitted. This process leaves a paper trail that provides a transparency acceptable to all stakeholders. © 2008 by Begell House, Inc.