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Background: We investigated the prevalence of psychiatric referral, frequency of repeat upper gastrointestinal (UGI) contrast studies, and esophagogastroduodenoscopy (EGD) in children with ineffective esophageal motility (IEM) before the confirmation of esophageal dysmotility. Methods: A total of 19 children (nine boys, 10 girls; mean age, 13.80 AE 5.10 years) with symptoms of refractory gastroesophageal reflux (GER) who underwent high-resolution esophageal impedance manometry (HRIM) were enrolled in this retrospective analysis. Refractory GER symptoms were defined as persistent symptoms even under acid-suppression therapy for 8 weeks in this study. Clinical data including age, gender, time from symptom onset to diagnosis, and number of UGI contrast studies and EGD before diagnosis were obtained. HRM parameters and the prevalence of psychiatric referral were also analyzed. Results: There are 14 children (73.68%) diagnosed with IEM by HRIM, and another 5 children (26.32%) diagnosed as GER disease (GERD) by EGD. A significant proportion of IEM children were misdiagnosed with psychological problems compared with the GERD children (78.57% vs 20.00%, P = 0.04). Three IEM children (21.43%) received antipsychotic and antidepressant agents before diagnosis of IEM, and all of them discontinued these medications after diagnosis. IEM children underwent a greater number of UGI contrast studies (1.07 AE 0.92 vs 0.20 AE 0.45; P = 0.02) and EGD (2.36 AE 2.50 vs 0.60 AE 0.55; P = 0.03) before HRM than GERD children. Conclusions: Esophageal manometry for the diagnosis of IEM should be considered in children with GER symptoms refractory to acid-suppression therapy for 8 weeks to avoid repeat UGI contrast studies, EGD, and psychological therapy.