Abstract Background Palatopharyngeal incoordination is a common phenomenon in patients requiring endotracheal intubation for mechanical ventilation. Understanding the underlying mechanism of palatopharyngeal incoordination may help as a screening tool that improves rates of early recognition and diagnosis and the ability to take preventive measures essential to alleviate related morbidity and complications. Objective The aim of this study is to screen palatopharyngeal incoordination in infants who needed mechanical ventilation and to elicit palatopharyngeal incoordination secondary to mechanical ventilation. Material and Methods This study included 51 patients at the Pediatric Intensive Care Unit, Faculty of Medicine, Ain Shams University, The study was conducted during the period from February 2021 to February 2022. patients were classified according to a Fiberoptic Flexible Endoscopic Evaluation of Swallowing (FEES) early post intubation, FEES early post extubation, Videofluoroscopic Swallow Study (VFSS) post extubation and dye study into five groups: group (1) the not affected group, group (2) the palatopharyngeal incoordination group, group (3) The palatopharyngeal incoordination with gastro esophageal reflux group, group (4) The reflux group, group (5) The congenital upper air way anomalies group in which patients were ventilated due to respiratory distress. Follow up FEES and VFSS were done after three months for palatopharyngeal incoordination patients. Results Palatopharyngeal incoordination was detected in 16 patients (31.3%), congenital upper airway anomalies were found in 12 patients (23.5%), and gastroesophageal reflux was only detected in 10 patients (19.6%). Performing VFSS and FEES after three months showed 92.3 % of palatopharyngeal incoordination patients had resolved palatopharyngeal incoordination and 7.7 % of palatopharyngeal incoordination patients had silent aspiration. Conclusion The prevalence of palatopharyngeal incoordination is 31.3 % and there was no palatopharyngeal incoordination secondary to mechanical ventilation.