The usefulness and accuracy of computer-assisted surgery have been evaluated clinically in many orthopedic fields, such as, joint replacement arthroplasty, cruciate ligament reconstruction, and pedicle screw placemen. Recently several preliminary reports have been issued on the application of navigation to bone tumor surgery. The main advantage of navigation-assisted bone tumor surgery is that it provides highly accurate three-dimensional radiological information for intraoperative guidance. In particular, distances from tumors to resection margins can be precisely determined using intraoperative three-dimensional images. Accordingly, the technique allows preservation of function to be maximized by minimizing unnecessary resection. However, surgeons should recognize that the accuracies of navigation systems in bone tumor surgery have some hidden pitfalls. Here, based on our clinical results, we describe the surgical techniques used and include some cautionary notes.