The aim of this study was to evaluate the results of Swallowing Rehabilitation Protocol (SRP) on swallowing function (SF) of esophageal atresia and tracheoesophageal fistula (EA-TEF) patients with pharyngeal swallowing disorder.  In this study, 24 children with EA-TEF who had deglutitive and respiratory problems were grouped into either study ( = 12) or control group ( = 12) by basic randomization. Study group received the SRP including neuromuscular electrical stimulation, thermal tactile stimulation, and hyolaryngeal mobilization. The control group received nonnutritive stimulations. SF was evaluated with 3 mL liquid and pudding barium by videofluoroscopic swallowing study (VFSS) before and after 20 sessions of interventions.  No statistical differences were found between groups in terms of descriptive characteristics including age, sex, weight, height, type of atresia, repair type, repair time, and start time of oral intake ( > 0.05). There were no statistical differences between groups in term of swallowing parameters ( > 0.05), except reflux ( = 0.004) according to VFSS findings. After 20 sessions of interventions, the study group showed improvement in penetration-aspiration scale scores, oral phase dysfunction, delay in swallowing reflex, and residue in valleculae and pyriform sinuses after pudding swallow. The control group showed improvement only in oral phase dysfunction.  SRP can be recommended to improve SF in patients with EA/TEF who have pharyngeal swallowing disorders.

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