Aim:When cerebellar tonsils are placed ≥ 5 mm below the foramen magnum, the situation is referred to as Chiari malformation Type I (CM-I). The prevalence of CM-I has been reported as 0.6%–1%. Due to obstruction in Cerebrospinal Fluid Circulation (CSF) circulation, formation of syrinx of the spinal cord can be observed in these patients. We aimed to ascertain whether the brain stem\'s shape differs in patients with syrinx and without syrinx, relative to healthy controls.Material and Methods:Data on marked brainstem regions were obtained from 2D digital image files. Generalized Procrustes analysis was used to evaluate shape differences among patients with syrinx, patients without syrinx, and healthy controls. Shape deformations among groups were examined by Thin Plate Spline (TPS) analysis. Results:According to the brain stem shape, there were differences between patients with syrinx and controls and between patients without syrinx and controls. High-level deformations were also observed among the groups.Conclusion:In the present study, the presence of shape deformations in Chiari patients\' brainstem was demonstrated. This is the first study using a landmark-based geometrical morphometric method to demonstrate the shape difference in Chiari patients\' brainstem.