While significant component malalignment in the frontal and sagittal plane may lead to early loosening and pain, even small errors in the rotational component alignment are not tolerated due to its complex impact on knee joint kinematics and especially the patella tracking. It is accepted that navigated implantation of total knee arthroplasties improves accuracy in the frontal plane but it is yet unclear weather navigation leads to a more precise rotational component alignment. The study evaluated the influence of navigated implantation on femoral and tibial component alignment. In a prospective randomized study 32 navigated and 28 conventionally implanted total knee arthroplasties were evaluated through a postoperative CT scan. In all cases the femoral component was referenced to the surgical epicondylar axis and the tibial component was referenced to the medial third of the tibial tuberosity. The angles between these bone landmarks and the components were measured on the CT scans and compared between both study groups. The rotational malalignment of the femoral component in the conventional operating technique was 0.1° ± 2.2° (range 3.3° of internal rotation and 5.0° of external rotation). Navigated implanted femoral components showed a malalignment of 0.3° ± 1.4° (range 4.7° of internal rotation and 2.2° of external rotation), the difference was not significant. The rotational malalignment of the tibial component in the conventional technique was 7.5° ± 6.0° (range 27.1° of internal rotation and 15° of external rotation). Navigated implanted tibial components showed a malalignment of 6.9° ± 4.7° (range 21.2° internal rotation and 11.0° external rotation), the difference was not significant. In conclusion the use of a navigation system did not improve the rotational alignment of the tibial or femoral component if only one bone landmark was used. Taking the relatively small errors of a navigation machine into account the error is attributable to the surgeon, who seems to be unable to precisely define bone landmarks. More than one landmark (e.g. additionally Whiteside’s line, posterior condyles, flexion gap for the femur and ankle joint for the tibia) should be used to define the component rotations. Consideration of different rotational landmarks is best done with a navigation system that, in contrast to the manual technique, has the possibility to show the degree of deviation of the components from each landmark.