Follow-up of children born with esophageal atresia (EA) is mandatory due to high incidence of comorbidities. We evaluated endoscopic findings at follow-up of EA patients performed at our Centre according to ESPGHAN-NASPGHAN 2016 guidelines. A retrospective observational study was performed using data from January 2016 to January 2021. We included EA patients (age range: 1–18 years) who were offered a program of endoscopic and histological high gastrointestinal (GI) tract examinations as per ESPGHAN-NASPGHAN 2016 guidelines. Clinical, surgical, auxological, endoscopic, and histological data were reviewed; variables as polyhydramnios, EA type, surgical type, enteral feeding introduction age, growth data, and symptoms were correlated to endoscopic and histological findings. The population included 75 patients (47 males), with mean age of 5 ± 4 years. In 40/75 (53.3%) patients, we recorded oral feeding problems, and upper gastrointestinal or respiratory symptoms suspicious of gastroesophageal reflux. Eosinophilic esophagitis (EoE) incidence was 9/75 (12%), significantly higher than in general population (p < 0.0001), and 10/75 (13.3%) presented non-specific duodenal mucosal lesions. EoE represents a frequent comorbidity of EA, as previously known. EA is also burdened by high, never-described incidence of non-specific duodenal mucosal lesions. Embedding high GI tract biopsies in EA endoscopic follow-up should be mandatory from pediatric age.