Failures of treatment of osteoid osteoma (OO) are related to errors in exact localization and incomplete excision of the nidus. Intraoperative Iso-C 3D navigation allows exact localization, excision and confirmation of excision by percutaneous methods. We report the successful percutaneous excision of OO in 11 patients (extremities-5; spine-6). All patients had a minimally invasive reflective array (MIRA) fixed to the same bone in the extremities and to the adjacent spinous process or body(caudal) in spine, followed by registration of anatomy. A tool navigator was utilized to plan the key hole incision so that the trajectory did not involve important anatomical structure. A sleeve was then introduced which allowed the usage of instruments like a burr and curette to deroof the nidus, curette the nidus and obtain material for histopathology and further burr the cavity to ensure complete eradication of the nidus. During the entire procedure, the tool navigator was used frequently to reconfirm the location and the depth of burring. Following excision, registration using Iso-C 3D C-arm was done to confirm the complete eradication of the nidus. The age of the patients varied from 10 years to 27 years. In the extremities, location of the MIRA was in the same bone and firm anchorage was obtained using either a single Steinman pin locator (4 patients) or a double pin locator (1 patient). In spine the MIRA was attached to the adjacent spinous process (caudal) in the cervical, thoracic or lumbar region (5 patients) and in sacrum (1 patient) it was attached using a Steinman pin to the adjacent vertebral body. Excellent three-dimensional view of the nidus and localization was possible in all patients. A safe trajectory that avoided anatomical structures was possible in all patients using a tool navigator. The incision ranged from 1 to 4 cms. Adequate material for histology was obtained in ten patients that confirmed the diagnosis of osteoid osteoma and in one patient histopathological confirmation was not possible because the nidus was completely destroyed during the process of deroofing and burring. In ten patients, post excision ISO-C 3D scans confirmed adequate removal and in one patient, it was successful in identifying incomplete removal requiring further excision of the nidus. The average operating time was 62 mins (37–90 mins) and the blood loss was less than 30 cc in all patients. All patients achieved excellent pain relief and were asymptomatic at an average follow up of 3.4 (2.2 – 3.9) years. Iso-C 3 D navigation offers the advantage of excellent localization of the nidus and percutaneous excision of these tumors, thereby conserving bone in critical locations like the spine and upper end of femur. It also offers the advantage of intraoperative confirmation of adequate excision and allows harvesting the nidus for histological confirmation.