We evaluated the postoperative alignment of 37 primary total knee arthroplasties performed using a computed tomography–based navigation system (Vector Vision Knee 1.5; Brain Lab, Germany) with a new 3-dimensional analysis. The mean coronal femoral angle was 89.0° ± 1.4° (85.5°-92.8°), and the coronal tibial component was 89.2° ± 1.0° (87.4°-91.6°). The hip-knee-ankle angle was observed to be 178.2° ± 1.5° (173.9°-181.8°). The external rotational alignment of the femoral component relative to the surgical epicondylar axis was −0.5° ± 1.7° (−3.2° to 3.4°). The results demonstrated that a computed tomography–based navigation system provided a reasonably satisfactory component alignment. The discrepancy between the 2-dimensional and 3-dimensional evaluations was 1.0° ± 0.9° (0.1°-3.4°). Three-dimensional analysis is necessary to evaluate the accuracy of the navigation system .