Purpose: to review recent literature concerning long-term health issues and transitional care in esophageal atresia (EA) patients. PubMed, Scopus, Embase and Web of Science databases were screened for studies regarding EA patients aged more than or equal to 11 years, published between August 2014 and June 2022. Sixteen studies involving 830 patients were analyzed. Mean age was 27.4 years (range 11–63). EA subtype distribution was: type C (48.8%), A (9.5%), D (1.9%), E (0.5%) and B (0.2%). 55% underwent primary repair, 34.3% delayed repair, 10.5% esophageal substitution. Mean follow-up was 27.2 years (range 11–63). Long-term sequelae were: gastro-esophageal reflux (41.4%), dysphagia (27.6%), esophagitis (12.4%), Barrett esophagus (8.1%), anastomotic stricture (4.8%); persistent cough (8.7%), recurrent infections (4.3%) and chronic respiratory diseases (5.5%). Musculo-skeletal deformities were present in 36 out of 74 reported cases. Reduced weight and height were detected in 13.3% and 6% cases, respectively. Impaired quality of life was reported in 9% of patients; 9.6% had diagnosis or raised risk of mental disorders. 10.3% of adult patients had no care provider. Meta-analysis was conducted on 816 patients. Estimated prevalences are: GERD 42.4%, dysphagia 57.8%, Barrett esophagus 12.4%, respiratory diseases 33.3%, neurological sequelae 11.7%, underweight 19.6%. Heterogeneity was substantial (> 50%).Conclusion: EA patients must continue follow-up beyond childhood, with a defined transitional-care path by a highly specialized multidisciplinary team due to the multiple long-term sequelae.What is Known:• Survival rates of esophageal atresia patients is now more than 90% thanks to the improvements in surgical techniques and intensive care, therefore patients’ needs throughout adolescence and adulthood must be taken into account.What is New:• This review, by summarizing recent literature concerning long term sequelae of esophageal atresia, may contribute to raise awareness on the importance of defining standardized protocols of transitional and adulthood care for esophageal atresia patients.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00431-023-04893-6.