Fundoplication alters the anatomy of the lower esophageal sphincter but should have no direct effects on motility distal to the sphincter. Of 55 children referred for evaluation of symptoms consistent with upper gastrointestinal motor dysfunction, 28 had undergone fundoplication 6 months to 4 years earlier to treat severe gastroesophageal reflux that had failed medical management. All 28 children had symptoms that were unchanged or worsened after fundoplication. In all children, we studied fasting and fed antroduodenal motility, and compared results from groups with and without fundoplication. Abnormalities in antroduodenal motility were found in 25 of 28 of the fundoplication group and in 25 of 27 of unoperated children. We found a wide range of abnormalities, but there were no differences in the types of severity of abnormalities between groups. In summary, in children with severe functional gastrointestinal symptoms, antroduodenal manometry uncovered physiological abnormalities, and fundoplication failed to relieve symptoms. These data suggest that preoperative intestinal manometry could identify children unlikely to benefit from fundoplication.