Background Sphincter of Oddi dysfunction (SOD) is a controversial topic, especially in patients with no objective findings on laboratory or imaging studies (SOD type III). The value of ERCP manometry with sphincterotomy is unproven and carries significant risks. Objective To describe the process of planning and initiating a randomized sham-controlled study to establish whether patients with SOD respond to sphincter ablation, and whether the outcomes are predicted by the pain patterns, presence or absence of other functional GI or psychosocial problems, or the results of manometry. Design Planning a trial to establish which patients with "suspected SOD" (if any) respond to endoscopic sphincter ablation. Setting Meetings and correspondence by a planning group of gastroenterologists and clinical research specialists hosted at the Medical University of South Carolina. Patients Clarifying subject characteristics and inclusion and exclusion criteria. Interventions Defining the questionnaires, therapies, randomizations, and numbers of subjects required by outcome measures. Defining the metrics of success and failure. Results The planning resulted in funding for the proposed study as a cooperative agreement with the National Institute of Diabetes and Digestive and Kidney Diseases. Limitations Lack of data required several consensus decisions in designing the protocol. Conclusion The planning process was challenging, and some changes were needed after initiation. (Clinical trial registration number: NCT00688662.) © 2010 American Society for Gastrointestinal Endoscopy.