EMRs, or electronic medical records, are frequently mentioned as an important new tool for integrating clinical trial capabilities into routine clinical practice. Nonetheless, consolidating clinical exploration and clinical consideration exercises into one brought together electronic data framework requires incorporating a significant group of administrative necessities and institutional strategies. In order for the EMR configuration to simultaneously meet all requirements, divergent interpretations of internal policies and external regulations must be reconciled. Additionally, attempts to implement potential policies in the EMR system revealed a number of commercial system limitations and inconsistencies. Until the commercial vendor provides the missing functionality, the authors describe a set of compromises that will be implemented at The Children's Hospital. Similar configuration and policy issues will need to be resolved at each facility of an EMRimplementing institution. Before incorporating translational research capabilities into an operational EMR, the authors present a list of questions that must be answered categorically in order to highlight these configuration difficulties.