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Esophageal duplication cysts (EDCs) are rare congenital anomalies that can be associated with symptomatic spinal abnormalities, but presentations due to EDC symptoms are rarely found in the presence of spinal abnormalities.A 6-month-old infant weighing approximately 5.0 kg presented with a 2-month pulmonary infection and more recent difficulty swallowing and nutritional intolerance that did not improve with medical treatment. Contrast-enhanced chest computed tomography showed a well-defined, mediastinal, homogeneous, low-density cystic mass of 11.9 × 5.5 × 5.1 cm, compressing the liver and bending the trachea forward. Hemivertebrae were present (T4 and T3). Diagnostic laparoscopy was performed, but was converted to open surgery. After ensuring that the cyst was not within the abdominal cavity, thoracotomy was performed, and the cyst was completely resected. Pathophysiological examination revealed an EDC. The patient recovered well, without symptoms 6 months later.Overall, noninvasive imaging and diagnostic procedures may not be sufficient to define the exact location of an EDC. Although hemivertebrae were present, they were asymptomatic and did not require treatment; only the EDC induced nonspecific symptoms that disappeared after surgery.