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Background: Long-gap esophageal atresia remains a challenging condition. There are no standard guidelines on the optimal surgical approach or the optimal management strategy for the potential postoperative complications. We report a case of long-gap EA treated by staged thoracoscopic repair in which the chest drain caused a complication. Case report: A female with prenatal diagnosis of polyhydramnios and a small stomach suspicious for esophageal atresia was delivered by cesarean section at 33 weeks of gestation. The orogastric tube remained coiled in the upper esophagus, confirming the diagnosis of esophageal atresia. X-rays showed a gasless abdomen, suspicious for a lack of a distal tracheo-esophageal fistula. On the second day of life, the patient underwent a tracheoscopy, which confirmed the absence of a tracheo-esophageal fistula. A gastrostomy was done at the same time. At 1 month of age the patient underwent a fluoroscopic study, and the esophageal gap was found to be 3.5 vertebral bodies. At 2 months of age she underwent a thoracoscopic placement of internal traction sutures. Five days later she underwent a thoracoscopic esophageal anastomosis, which was under moderate tension. A chest tube was left in place. Seven days after the operation a routine esophagram showed that the chest tube had slipped into the esophagus through the anastomosis. We pulled the chest tube back under direct endoscopic vision. There was also a tight stenosis at the anastomosis. We placed a trans-anastomotic tube for feedings and a naso-esophageal tube to suction the secretions of the upper esophagus. Forty-for days later we repeated the esophagram and confirmed the persistence of the tight stenosis. The patient underwent serial dilations every 2 weeks for 3 months and a Nissen fundoplication, after which the stricture completely resolved. Conclusion: Although rare, the chest tubes used after the repair of an esophageal atresia can cause complication at the anastomotic site.