OsteogenesisImperfecta (OI) is a rare disease with respiratory problems, which are usually attributed to the secondary effects of scoliosis and rib fractures and to severe restrictive pulmonary disease. Conventional morphometry has already been studied in OI patients but three-dimensional geometric morphometrics (3D GMM) has never been used to assess how the thoracic spine shape changes during maximal breathing. A total of 6 adult subjects with OI type III and 16 healthy controls underwent a spirometric study and two computed tomography scans in maximal inspiration and expiration. Shape data by means of 3D GMM and Cobb angle values of scoliosis and kyphosis were obtained and their relationship with spirometric values was analysed using regressions and mean shape comparisons. No differences in kyphosis (p = 0.285) and scoliosis Cobb values (p = 0.407) were found between inspiration and expiration in OI patients. The 3D GMM analysis revealed significant shape differences between OI and control subjects (p < 0.001) that were related to the inspiration (p = 0.030) and not to the expiration (p = 0.079). Nevertheless, no significant relation was found between thoracic spine shape, scoliosis, kyphosis and breathing outcomes in both OI patients and controls. There were thoracic spine shape differences during maximal breathing between OI patients and controls that were mainly related to the inspiration.