Abstract Objective To assess the prevalence of abnormal gastric emptying and small bowel transit in children with functional dyspepsia at a tertiary care center, and the relationship between abnormal gastric and small bowel transit and symptoms in pediatric patients with functional gastrointestinal disorders. Study design Patients were selected by a cross-sectional chart review based on the following inclusion criteria: (1) completion of scintigraphic study of the gastric emptying of solids at 2 hours (GE2), 4 hours (GE4), and small bowel transit at 6 hours (SBT) using a standardized egg meal labeled with 99mTechnetium sulfur colloid, and (2) gastrointestinal (GI) complaints without mucosal or organic disease. Logistic regression analysis was used to assess the association between the presence of upper GI symptoms, and each parameter of gastric and small bowel transit. Results Children with upper GI symptoms (n=96) were identified. Among 57 children with functional dyspepsia, 40% had slow SBT. Fast GE at 4 hours, and slow SBT were independently associated with bloating. Children with fast SBT were less likely to report abdominal pain. Conclusion Incorporating assessments of gastric and small bowel transit may be useful in the evaluation of pediatric patients with upper GI symptoms and functional dyspepsia.