Investigator-initiated clinical trials represent a small but extremely important portion of medical research. In the process of translating basic science discoveries to novel therapies, new drugs or devices may be developed and tested. In light of increased compliance scrutiny, the need to streamline research projects, and the growing complexity of the U.S. Food and Drug Administration's (FDA's) regulations, the research leadership at the University of Minnesota Academic Health Center (AHC) determined in 2002 that a service should be established to address these issues. The assumption was that providing a service to assist researchers with regulatory obligations would result in additional clinical research that might not have been pursued due to perceived regulatory hurdles. The authors present an overview of the FDA regulatory process as it applies to investigator-initiated research involving investigational new drugs and investigational medical devices. The rationale for creating a program designed specifically to assist faculty with investigational new drug (IND) applications and investigational device exemption (IDE) applications is discussed. The services provided by the IND/IDE Assistance Program (IAP) at the University of Minnesota Academic Health Center are described. The value of the IAP to the AHC is presented along with examples of successes attributable to the IAP and lessons learned so far. Since the establishment of the IAP several issues that might have placed the university at risk have been identified. These issues have been addressed to help improve the ease in which investigator-initiated research is conducted and compliance is maintained.