We compared the alignment of 39 total knee replacements implanted using the conventional alignment guide system with 37 implanted using a CT-based navigation system, performed by a single surgeon. The knees were evaluated using full-length weight-bearing anteroposterior radiographs, lateral radiographs and CT scans. The mean hip-knee-ankle angle, coronal femoral component angle and coronal tibial component angle were 181.8° (174.2° to 188.3°), 88.5° (84.0° to 91.8°) and 89.7° (86.3° to 95.1°), respectively for the conventional group and 180.8° (178.2° to 185.1°), 89.3° (85.8° to 92.0°) and 89.9° (88.0° to 93.0°), respectively for the navigated group. The mean sagittal femoral component angle was 85.5° (80.6° to 92.8°) for the conventional group and 89.6° (85.5° to 94.0°) for the navigated group. The mean rotational femoral and tibial component angles were −0.7° (−8.8° to 9.8°) and −3.3° (−16.8° to 5.8°) for the conventional group and −0.6° (−3.5° to 3.0°) and 0.3° (−5.3° to 7.7°) for the navigated group. The ideal angles of all alignments in the navigated group were obtained at significantly higher rates than in the conventional group. Our results demonstrated significant improvements in component positioning with a CT-based navigation system, especially with respect to rotational alignment.