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Background: Neuromuscular Scoliosis is a frequent complication of Cerebral Palsy that requires surgical management including spinal fusion. The objective of this observational study was to describe differences in the frequency of postoperative complications in children with Cerebral Palsy following spinal fusion surgery compared to children with Idiopathic Scoliosis. Methods: The 2016 Kids’ Inpatient Database was queried to identify pediatric patients (old) with concurrent diagnoses of Cerebral Palsy and Neuromuscular Scoliosis undergoing spinal fusion surgery. Cases were compared to children without Cerebral Palsy and with a diagnosis of Idiopathic Scoliosis undergoing the same procedure. Fitted Poisson regression analysis with robust variance was performed to estimate relative risks in the frequency of various clinical complications while adjusting for several potentially confounding variables of importance. Results: A total of 660 cases and 5,244 comparators were identified. Compared to children with Idiopathic Scoliosis, children with Cerebral Palsy were younger (13.6 vs. 14.3 years), more likely to be male (54% vs. 23%), and more likely to have had governmental insurance (52% vs. 32%). They also had longer hospital lengths of stay (8 days vs. 4 days). After adjusting for a number of potentially confounding sociodemographic and clinical variables, children with Cerebral Palsy were more likely to have postoperative pulmonary, gastrointestinal, and surgical complications, receive blood transfusions, and be admitted to the ICU. Conclusions: Children with Cerebral Palsy have an increased risk of complications following spinal fusion surgery leading to longer hospital stays. These results further inform surgical decision-making and anticipatory guidance for these children and their caregivers.