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Background: Atlantoaxial subluxation (AAS) is a diagnosis describing misalignment of the C1 vertebra relative to C2. Excessive translation of this joint, located adjacent to the medullary brain stem, can lead to devastating neurological consequences. A higher prevalence of AAS within the Down syndrome (DS) population has been well-established. This study aims to establish a prevalence rate of DS in patients hospitalized for AAS and compare outcomes between AAS patients with and without DS. Methods: This study utilized the National Inpatient Sample (NIS) provided by the Healthcare Cost and Utilization Project (HCUP). In accordance with HCUP 2023 Clinical Classifications Software Refined files, data were queried using the International Classification of Diseases 10th Edition codes for DS and AAS. Demographics, comorbidities, hospital course, and outcomes were examined and compared using binary and linear multivariate regression. IBM SPSS software was used for data analysis. Results: Of the 213,095 patients in the NIS database admitted between 2016 and 2020 with AAS as their primary diagnosis, 7.2% were DS patients. DS patients were significantly younger (26.56 ± 20.81 vs. 49.39 ± 27.63, P < 0.01), less likely to be female (33.30% vs. 52.10%), and had fewer comorbidities (diabetes mellitus, hypertension, and hyperlipidemia) than non-DS patients. There was no significant difference in likelihood to undergo surgical fusion between DS patients and non-DS patients with AAS. Conclusion: This large-scale study using NIS data determined that 7.2% of all patients admitted to hospitals for AAS are DS patients. The analysis of demographics, hospital course, and outcomes can influence the development of treatment protocols for AAS in the DS population.