BACKGROUND: Given the high prevalence and complication risks of acid gastroesophageal reflux (GERD) in the first months of life in infants with esophageal atresia, the ESPGHAN/NASPGHAN consensus statement recommends systematic treatment with proton pump inhibitors (PPIs) until the age of 1 year and checking for acid GERD thereafter. However, these recommendations have not been evaluated. METHODS: This prospective study was conducted from 2007 to 2016. We evaluated the prevalence of acid GERD in 100 consecutive infants presenting with esophageal atresia/tracheoesophageal fistula after the age of 18 months when PPI treatment was stopped. The diagnosis of acid GERD was based on positive pH-metry and/or evidence of complications (e.g., peptic esophagitis, need for jejunal nutrition, or antireflux surgery). Those with acid GERD at a median age of 18 months received a control examination every year or adapted to their clinical situation. RESULTS: The prevalence rates of acid GERD were 64.3% at 18 months and 22.8% at the last follow-up (median age 65 months).There is no risk factor for acid GERD identified. CONCLUSIONS: This study shows a high prevalence of acid GERD in late infancy and supports the recommendation of systematic checking for acid GERD when treatment with PPI is stopped. IMPACT: Acid gastroesophageal reflux disease (GERD) is a frequent complication of esophageal atresia in infants. The ESPGHAN/NASPGHAN consensus, which is based on expert opinion, recommends systematic treatment of children with PPI until the age of 1 year. The prevalence rates of acid GERD were 64.3% at 18 months and 22.8% at the last follow-up. This study shows a high prevalence of acid GERD in late infancy and supports the recommendation of systematic checking for acid GERD when treatment with PPI is stopped.