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 degrees +/- 1.4 degrees (85.5 degrees -92.8 degrees ), and the coronal tibial component was 89.2 degrees +/- 1.0 degrees (87.4 degrees -91.6 degrees ). The hip-knee-ankle angle was observed to be 178.2 degrees +/- 1.5 degrees (173.9 degrees -181.8 degrees ). The external rotational alignment of the femoral component relative to the surgical epicondylar axis was -0.5 degrees +/- 1.7 degrees (-3.2 degrees to 3.4 degrees ). 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 degrees +/- 0.9 degrees (0.1 degrees -3.4 degrees ). Three-dimensional analysis is necessary to evaluate the accuracy of the navigation system.