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. 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. 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. 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. 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.