The objective of this study was to develop a method to assess the accuracy of an electromagnetic technology image-free navigation system for total knee arthroplasty in a leg with normal or abnormal mechanical alignment. An acrylic phantom leg was constructed to simulate tibia and femur deformation. Determination of actual leg alignment was achieved using a digital caliper unit. In the setting of normal alignment, the mean error of the system characterised as the difference between the measured computer navigation and digital caliper angles ranged between 0.8 degrees (frontal plane) and 1.5 degrees (lateral plane). In the setting of abnormal alignment, the mean error ranged between 0.4 degrees (frontal plane) and 1.6 degrees (lateral plane). Deformity had no demonstrable effect on accuracy. The study demonstrates satisfactory in vitro system accuracy in both normal and abnormal leg mechanical alignment settings.