Infants with history of prematurity, neurological impairment and under critically illness have higher risk of gastroesophageal reflux disease (GERD) and often presented with extraesophageal manifestations. This retrospective study enrolled 79 infants less than 1 year of age (corrected age for prematurity) referred for 24-hour MII-pH monitoring. Prematurity (65.8%), laryngomalacia (46.5%), and neurological impairment (40.5%) were the most common three comorbidities. Abnormal MII-pH monitoring was detected in 39.2% of study subjects, significantly higher in those presenting with esophageal symptom presentation (P = 0.038). Positive pressure ventilation and feeding tube support were significantly associated with less acidic and weakly acidic reflux episodes. Underweight and neurological impairment were identified to be the most important factors for predicting abnormal MII-pH monitoring in overall and extra-esophageal symptom presented infants, respectively. In conclusion, infants presenting with esophageal symptoms or underweight have higher risk of abnormal MII-pH study, whereas extra-esophageal symptoms presented infants comorbid with neurological impairment appear to have normal results. A 24-hour MII-pH study provides a comprehensive evaluation of reflux in the esophagus, determining subsequent anti-reflux therapy or other management strategies for those GER-like symptoms.