We have assessed the bone cuts achieved at surgery compared to the planned cuts produced during computer assisted surgery (CAS) using a CT free navigation system. In addition, two groups of matched patients were compared to assess the post-operative mechanical alignment achieved: 14 patients received a LCS total knee replacement (TKR) using the VectorVision module and 14 received a TKR using a conventional method of extramedullary alignment jigs The deviation in each plane (valgus-varus, flexion-extension and proximal-distal) was calculated. For the tibia the mean deviation in the coronal plane was 0.21 degrees of Varus (SD = 1.37) and in the sagittal plane was 1.29 degrees of flexion (SD = 3.73) and 0.24 mm of resection distal to the anticipated cut (SD = 2.14). For the femur the mean deviation in the coronal plane was 0.88 degrees (SD = 2.2) of valgus and in the sagittal plane the mean deviation was 0.3 degrees (SD = 2.91) of extension. In the transverse plane there was a mean deviation of 0.07 degrees (SD = 1.57) of external rotation. There was mean deviation of 2.33 mm of proximal resection (SD = 2.9) and 1.05 mm of anterior shift (SD = 2.81). On comparing the two groups, no statistically significant differences were found for the angles between the femoral component and the femoral mechanical axis, the tibial component and the tibial mechanical axis, the femoral and tibial mechanical axis and the femoral and tibial anatomical axis. We have demonstrated variation in the true bone cuts obtained using computer assisted surgery from those suggested by the software and have not demonstrated significant improvement in post-operative alignment. Justification for the extra cost, time and morbidity associated with this technology must be provided in the form of improved clinical outcomes in the future.