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Esophageal atresia is rare, but improved surgical and intensive care techniques have increased rates of survival in children, so there are now many adults with this disorder. Many patients with esophageal atresia develop gastroesophageal reflux (GER), raising concerns about increased risk of Barrett’s esophagus (BE; prevalence of 1.3%–1.6% in general population) and esophageal carcinoma. We assessed the prevalence of BE and esophageal carcinoma in this population.We performed a prospective study of 289 patients with esophageal atresia at the Department of Gastroenterology and Hepatology at Erasmus MC University Medical Center in The Netherlands, from May 2012 through March 2017. A total of 151 (median age, 25.4 y; age range, 16.8–68.6 y) underwent upper endoscopies as part of a surveillance program for (pre)malignant esophageal lesions. Biopsies were collected and analyzed by histology. We collected data on patients’ use of medications, tobacco, and alcohol; gastrointestinal symptoms; ability to swallow; complaints of GER; and type of atresia and surgeries. Prevalence of esophageal squamous cell carcinoma (ESCC) was determined using data from The Netherlands Cancer Registry. The number of persons alive on January 1, 2016, in the esophageal atresia cohort and in the general Dutch population were used to calculate the 10-year prevalence of ESCC per 100,000 persons in both populations.Forty-seven percent of patients with esophageal atresia had a history of GER and 20.5% had undergone fundoplication surgery. Endoscopy revealed normal esophagus in 68.2% of patients, esophagitis in 7.3%, and columnar-lined esophagus in 24.5%. Histology revealed normal mucosa in 50.3% of patients, esophagitis in 23.2%, gastric metaplasia in 17.2%, and BE in 6.6% (at a median age of 31.6 years). A history of fundoplication surgery was associated with BE (P = .03). Three ESCCs developed, in 2 men, at ages 42, 44, and 60 years. This corresponded to a prevalence of 0.7% in patients with esophageal atresia—a value 108-fold higher than in the same age group in the general population.The prevalence of BE is 4-fold higher in young adults with esophageal atresia, and the prevalence of ESCC is 108-fold higher than in the general population. This finding could have important implications for transition of young adults from pediatric care to adult gastroenterology departments to receive life-long endoscopic follow-up evaluation to facilitate early diagnosis of relevant lesions.