The aim of this paper was to analyse the vertebral morphometry in idiopathic scoliosis with respect to pedicle screw instrumentation by means of computed tomography scans. The pedicle morphometry between T5 and L4 was analysed by computed tomography scans in 29 surgically treated patients with idiopathic right thoracic scoliosis. Measurements included chord length, endosteal transverse pedicle diameter and transverse pedicle angle. The endosteal transverse pedicle diameter was significantly smaller (P<0.05) on the concavity in the apical region of the thoracic spine. The chord length was the shortest at the fifth thoracic vertebra with significantly larger dimensions on the concavity of the apical region in the thoracic spine (P<0.05). The transverse pedicle angle varied between 6° in the lower thoracic spine and 12° at the upper thoracic and lower lumbar spine. The morphometry in scoliotic vertebrae is substantially different from those in normal spines with an asymmetrical intra-vertebral deformity. Pedicle screw instrumentation in the middle thoracic spine appears critical due to the small endosteal pedicle diameter, especially on the concave side.