The most difficult aspect of financial conflict of interest (FCOI) and compliance with federal regulations involves the assessment and management of identified FCOIs. While some federal agencies provide examples of the structure and content of management plans, it is up to institutions to evaluate FCOI to determine whether and how research may be conducted when conflict is present. Unfortunately, there is minimal federal guidance on the evaluation and management aspect of FCOI and institutions must carefully consider and implement appropriate procedures to ensure compliance. Once a conflict has been disclosed and is known by the institution, the burden of responsibility falls squarely on the institution. Without clear direction from federal agencies, institutions may become paralyzed with indecision or refuse to allow any research to proceed where there is known conflict. Sources exist which provide some guidance on how to mitigate conflicts of interest. This paper provides information and steps to assist institutions with the evaluation and management of FCOI.