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Purpose: We aimed to identify the risk factors for thoracic and spinal deformities following lung resection during childhood and to elucidate whether thoracoscopic surgery reduces the risk of complications after lung resection., Methods: We retrospectively examined the medical records of all pediatric patients who underwent lung resection for congenital lung disease at our institution between 1989 and 2014., Results: Seventy-four patients underwent lung resection during the study period and were followed-up. The median age of the patients at the time of surgery was 5 months (range 1 day-13 years), and 22 were neonates. Thoracotomy and thoracoscopy were performed in 25 and 49 patients, respectively. Thoracic or spinal deformities occurred in 28 of the 74 patients (37%). Univariate analyses identified thoracotomy, being a neonate (age: <1 month) at the time of surgery, and being symptomatic at the time of surgery as risk factors for these deformities. However, a multivariate analysis indicated that only thoracotomy and being a neonate were risk factors for deformities., Conclusions: Thoracoscopic surgery reduced the risk of thoracic and spinal deformities following lung resection in children. We suggest that, where possible, lung resection should be avoided until 2 or 3 months of age.