Alternative approaches to the standard posterolateral incision for thoracotomy have been developed to minimize its postoperative pain and wound related side effects. Muscle-sparing (MS) thoracotomy has been a well-known substitution to the standard posterolateral thoracotomy for this purpose; however it has not been studied in the pediatric age group in detail. We studied retrospectively the patients with thoracotomy for non-cardiac, thoracic surgical procedures. Group 1 included the patients with standard posterolateral thoracotomy for the surgery. The patients with MS thoracotomy composed group 2. The related data were collected retrospectively. The early postoperative morbidities (time requiring for regaining shoulder girdle movement, extubation, intensive care unit stay, and hospital stay) and late musculoskeletal anomalies (scoliosis, elevation of the shoulder, winged scapula, asymmetry of the nipples) were compared between groups. A total of 90 patients were included in the study. Group 1 constituted 50 patients with an average age of 4.24 +/- 2.91 years. Group 2 included 40 patients with an average age of 4.20 +/- 2.92 years. Comparison of the demographics and the baseline characteristics of the patients were not different between groups. In comparison of operative characteristics, there was lesser morbidity in group 2 as re-exploration for bleeding, wound infection, wound healing and fewer intensive care unit and hospital stay days. Late follow-up revealed a significant increase in musculoskeletal deformities in group 1. We conclude that muscle-sparing incision should be preferred to the standard posterolateral thoracotomy in pediatric age.