Prospective clinical trials are a key step in translating bench findings into bedside therapies. Electronic medical records (EMRs) are often cited as a significant new tool for advancing clinical trial capabilities into standard clinical practice. However, combining clinical research and clinical care activities into one unified electronic information system requires integrating a substantial body of regulatory requirements and institutional policies. Differing interpretations of external regulations and internal policies need to be reconciled so that the EMR configuration simultaneously conforms to all requirements. The authors describe how they used a detailed clinical vignette to help focus discussions about their institution's current research policies and how regulations and policies might be implemented in a commercial EMR. The vignette highlighted a number of inconsistencies in the institution's policies and in individual interpretations of regulatory intent. Attempts to implement potential policies in the EMR system also revealed a number of limitations and inconsistencies in the commercial system. The authors describe a set of compromises that will be implemented at The Children's Hospital until missing functionality is made available from the commercial vendor. Each institution that implements an EMR will need to resolve similar policy and configuration issues at its own facility. The authors highlight these configuration challenges by presenting a list of questions that must be answered unambiguously before implementing translational research capabilities into an operational EMR.