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Osteoid osteomas are well known for intraoperative technical difficulties for localization and adequate excision, especially when they are not clearly visualized on plain radiographs or when they occur in difficult and inaccessible situations. Localization in the radiology suite and shifting the patient to the operating room can be cumbersome, and can result in errors because of lack of real-time imaging. In these scenarios, intraoperative navigation will be useful. We report a technique of intraoperative computed tomography (CT) navigation for localization and excision of osteoid osteomas of the long bones. Six patients (four femoral and two tibial lesions) with a radiological diagnosis of osteoid osteoma, in whom the nidus could not be visualized clearly on plain radiographs, were treated with this technique. Intraoperative CT navigation with AIRO was performed and the images were registered to the computer. The lesion was then localized and excised using a high-speed burr. All patients underwent postexcision on-table CT scans, which showed complete excision of the nidus. All patients became symptom free and are doing well at a minimum follow-up of 6 months. Intraoperative CT navigation helps to exactly localize the nidus and also helps to confirm complete excision of the nidus. This is a safe, effective and minimally invasive method to treat osteoid osteomas, particularly those that are not amenable to excision under C arm guidance.