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Objectives To conduct a pilot study examining whether adding biofeedback-assisted relaxation training (BART) to medication treatment results in better clinical outcomes than medication treatment alone for children with functional dyspepsia (FD) associated with duodenal eosinophilia, a subgroup of children with recurrent abdominal pain. Methods Twenty children were randomly assigned to receive a standardized medication treatment or medication plus 10 sessions of BART. Children and parents completed psychosocial functioning and quality of life measures at baseline, posttreatment, and 6 months. Children rated pain daily via PDA. Physicians provided biweekly assessments of clinical improvement. Results Children receiving medication plus BART demonstrated better outcomes on pain intensity, duration of pain episodes, and clinical improvement than children receiving medication alone. Conclusions BART is a promising adjunctive treatment for pediatric FD associated with duodenal eosinophilia. Electronic daily diaries appear to be a useful approach to assessing changes in self-reported pain ratings in this population.