In this prospective, randomized, controlled study, we compared the performance of conventional and navigated total knee arthroplasties. Component alignment was measured in 60 patients operated on using navigation and in 60 patients operated on using the conventional technique. The groups then were divided into a subpopulation to measure alignments of the distal femoral cuts in the three anatomic planes, the proximal tibial cut in the frontal and sagittal planes, and the resulting lower limb mechanical axis in the frontal plane. Postoperative weightbearing long-view radiographs were evaluated as were clinical results using three standard questionnaires at 28 months followup. The intraoperative measurements (mean +/- standard deviation) at the resection planes showed navigated surgeries result in more accurate alignments than conventional surgeries for the femur: in the frontal plane, 0.1 degrees +/- 0.9 degrees and 0.7 degrees +/- 1.6 degrees valgus, respectively; in the sagittal plane, 1.1 degrees +/- 1.8 degrees and 2.8 degrees +/- 2.0 degrees flexion; and in the transversal plane, 0.1 degrees +/- 1.2 degrees and 0.9 degrees +/- 1.7 degrees internal rotation. The navigated technique also reduced the number of cases with final mechanical axes greater than 3 degrees from 20.0% to 1.7%. Postoperative radiographs showed better component alignment using navigation, particularly at the femur. However, clinical scoring systems showed this radiographic improvement did not necessarily result in a better clinical outcome at short-term followup.