This study was undertaken to obtain and analyse, on the basis of sex, three-dimensional (3D) reconstructions obtained by a 3D computer program from two-dimensional (2D) vertebral column sections taken by multidetector computed tomography (MDCT) images, in the chinchilla. A total of 16 adult chinchillas (Chinchilla lanigera) of both sexes were used. The MDCT images were taken under general anaesthesia, and were then transferred to a personal computer on which 3D reconstructions were carried out using a 3D modelling program (Mimics 13.1). The volume, surface area and vertebral body length of each vertebra (except caudal region) forming the vertebral column were measured from the 3D models created. The ratios (in percentage) of the measurements of each vertebra (except the sacral ones) forming the vertebral column region (cervical part, thoracic part, lumbar part) were determined for statistical analysis. We detected significant differences (P < 0.05) between sexes in all vertebrae forming the vertebral column of the chinchilla with respect to volume, surface area and vertebral body length, except for C6 and L1. This study is the first to carry out 3D reconstructions of data obtained from CT images in the chinchilla and the obtained results contribute to a more detailed understanding of the anatomy of this species. Our strategy may also be useful for the design of experiments exploring the vertebral column in domestic mammals and humans.