To evaluate the three-dimensional (3D) characteristics of spine deformity in patients with non-idiopathic scoliosis compared with those observed in patients with adolescent idiopathic scoliosis (AIS). A retrospective chart review was conducted to identify patients with non-idiopathic scoliosis. Twenty-eight patients with neural axis (NA) abnormalities (Chiari 1, syrinx) and 20 patients with connective tissue disorder (CTD) (Marfan's, Beal's, Ehlers-Danlos syndrome, mixed) were identified. The 3D parameters of the coronal, sagittal, and axial plane were compared with 284 AIS patients with a similar range of coronal deformity. The average coronal curve was similar between all three groups (AIS 48 ± 15°, CTD 43 ± 22°, and NA 49 ± 18°; p = 0.4). The NA patients had significantly greater 3D thoracic kyphosis (20 ± 18° vs 10 ± 15°, p = 0.001) and less thoracic apical vertebral rotation (- 5 ± 18° vs - 12 ± 10°, p = 0.003) when compared with AIS. The CTD group's 3D thoracic kyphosis (p = 0.7) and apical vertebral rotation (p = 0.09) did not significantly differ from AIS. Significant negative correlations were found in all three groups between thoracic kyphosis and coronal curve magnitude (AIS r = - 0.49, CTD r = - 0.772, NA r = -0.677, all p < 0.001). Scoliotic patients with NA abnormalities have a more kyphotic, less-rotated 3D profile than patients with AIS, while scoliosis patients with CTD have 3D features similar to AIS. Irrespective of the underlying diagnosis, however, greater scoliotic curves were associated with a greater loss of intersegmental kyphosis, suggesting a similar biomechanical pathophysiology for curve progression.