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Background:. Computer-assisted surgery (CAS) can improve surgical precision in orthopaedic oncology. Accurate alignment of the patient’s imaging coordinates with the anatomy, known as registration, is one of the most challenging aspects of CAS and can be associated with substantial error. Using intraoperative, on-the-table, cone-beam computed tomography (CBCT), we performed a pilot clinical study to validate a method for automatic intraoperative registration. Methods:. Patients who were ≥18 years of age, had benign bone tumors, and underwent resection were prospectively enrolled. In addition to inserting a navigation tracking tool into the exposed bone adjacent to the surgical field, 2 custom plastic ULTEM tracking tools (UTTs) were attached to each patient’s skin adjacent to the tumor using an adhesive. These were automatically localized within the 3-dimensional CBCT volume to be used as image landmarks for registration, and the corresponding tracker landmarks were captured using an infrared camera. The main outcomes were the fiducial registration error (FRE) and the target registration error (TRE). The navigation time was recorded. Results:. Thirteen patients with benign tumors in the femur (n = 10), tibia (n = 2), and humerus (n = 1) underwent navigation-assisted resections. The mean values were 0.67 ± 0.15 mm (range, 0.47 to 0.97 mm) for FRE and 0.83 ± 0.51 mm (range, 0.42 to 2.28 mm) for TRE. Registration was successful in all cases. The mean time for CBCT imaging and tracker registration was 7.5 minutes. Conclusions:. We present a novel automatic registration method for CAS exploiting intraoperative CBCT capabilities, which provided improved accuracy and reduced operative times compared with more traditional methods. Clinical Relevance:. This proof-of-principle study validated a novel process for automatic registration to improve the accuracy of resecting bone tumors using a surgical navigation system.