Background Bone tumor resections for limb salvage have become standard treatment. Recently, computer-assisted navigation has been introduced to improve the accuracy of joint arthroplasty and possible tumor resection surgery; however, like with any new technology, its benefits and limitations need to be characterized for surgeons to make informed decisions about whether to use it. Questions/purposes We wanted to (1) assess the technical problems associated with computer-assisted navigation; (2) assess the accuracy of the registration technique; (3) define the time required to perform a navigated resection in orthopedic oncology; and (4) the frequency of complications such as local recurrence, infection, nonunion, fracture, and articular collapse after tumor resection and bone reconstruction with allografts using intraoperative navigation assistance. Methods We analyzed 69 consecutive patients with bone tumors of the extremities that were reconstructed with massive bone allografts using intraoperative navigation assistance with a minimum followup of 12 months (mean, 29 months; range, 12-43 months). All patients had their tumors reconstructed in three-dimensional format in a virtual platform and planning was performed to determine the osteotomy position according to oncology margins in a CT-MRI image fusion. Tumor resections and allograft reconstructions were performed using a computer navigation system according to the previously planned cuts. We analyzed intraoperative data such as technical problems related to the navigation procedure, registration technique error, length of time for the navigation procedure, and postoperative complications such as local recurrence, infection, nonunion, fracture, and articular collapse. Results In three patients (4%), the navigation was not carried out as a result of technical problems. Of the 66 cases in which navigation was performed, the mean registration error was 0.65 mm (range, 0.3-1.2 mm). The mean required time for navigation procedures, including bone resection and allograft reconstruction during surgery, was 35 minutes (range, 18-65 minutes). Complications that required a second surgical procedure were recorded for nine patients including one local recurrence, one infection, two fractures, one articular collapse, and four nonunions. In two of these nine patients, the allograft needed to be removed. At latest followup, three patients died of their original disease. Conclusions The navigation procedure could not be performed for technical reasons in 4% of the series. The mean registration error was 0.65 mm in this series and the navigation procedure itself adds a mean of 35 minutes during