A wide range of species, from chickens to pigs have been used as model systems for studying spinal deformities. However most of these models focus on the etiology of the problem, and few studies examine the effects of spinal deformities on locomotion. The goal of this study was to create a 3D geometrical description of the zebrafish musculoskeletal system using Micro CT imaging technology as a basis for comparing normal zebrafish and zebrafish with spinal deformities. Specifically, for use in developing a model as a basis for testing the functional consequences of spinal deformities. Large 3D deformities and structural differences were observed in the vertebral column of the scoliotic fish relative to the normal fish. Also, further analysis of the structural differences revealed that the facets of the vertebrae in the deformed spinal sections were fused with rays extending from both the dorsal and anal fins of the zebrafish with spinal deformities, which could translate to changes in the normal function, and could affect the survivability of affected individuals.