The position of the acetabular component affects the result of total hip arthroplasty(THA) in terms of postoperative dislocation, impingement, wear etc. However, as it is much difficult to place the component in the appropriate position for the cases of severe acetabular deformity, we used a Computed tomography(CT)-based navigation for THA in such cases. Therefore, the purpose of this study was to estimate the accuracy of a CT-based navigation in terms of acetabular component positioning in THA for severe acetabular deformities. 13 patients (1 man, 12 women), 14 hips underwent THA using a posterolateral approach with a CT-based navigation. The diagnoses were severe developmental dysplasia (Crowe group III, IV) in 6, ankylosis in 3, destructive arthritis after infection in 2, Charcot joint, and arthrodesed hip. And, we evaluated the differences of component position from the center of the anterior pelvic plane(APP), anteversion angle, and inclination angle relative to APP between the intraoperative data from the navigation system and the data from postoperative CT. Considering the intra-observer error, the measurement was done three times respectively and the mean value was accepted. We also estimated the difference between the component size planned and that implanted. The mean difference between intraoperative records and actual postoperative results of the component position shows 3.3 mm(range: 0–7.0, SD: 2.2) for the horizontal position, 3.2 mm(range: 0–9.7, SD: 4.5) for the vertical position, 4.4 mm(range: 2.0–7.7, SD: 1.6) for the antero-posterior position from the center of the APP, 1.3 degrees(range: 0–3.0, SD: 0.9) for the inclination and 2.9 degrees(range: 0.3–8.3, SD: 2.2) for the anteversion respectively. All components were placed in the safe zone by Lewinnek. The component size was predicted in 10/14(71.4%) hips. There were no complications related to the use of the navigation. This study showed the accuracy of cup positioning using a CT-based navigation in THA for the cases of severe acetabular deformity. We concluded that this system was a useful tool for surgeon to identify orientation, implant acetabular component at the precise position and angle, and to reduce the incidence of some complications especially for patients with these severe acetabular deformities.