PURPOSE: The flexion-extension axis (FEA) of the femur is substantially changed after mechanically aligned total knee arthroplasty (TKA) due to a discrepancy in bone cut thickness between the posterior and distal femoral regions. This study assessed the bony gap changes and FEA displacement caused by this problem in osteoarthritis patients. METHODS: The study enrolled 60 knees from 60 patients for whom primary TKA was planned due to medial knee osteoarthritis. All patients underwent computed tomography, and 3-dimensional (3D) bone models were reconstructed on 3D-planning software. Bone cuts of the distal femur and proximal tibia were simulated to be perpendicular to each mechanical axis. Bony gap change was computed as the difference in bone cut thickness between medial and lateral compartments. Each femoral condyle was assessed for potential FEA displacement, as the difference in bone cut thickness between posterior and distal femoral regions. RESULTS: The mean magnitude of bony gap discrepancy necessary for mediolateral balancing was 1.6 ± 3.3 mm (range -7 to 8.2 mm) at 0° extension and -0.2 ± 2.6 mm (range -6.4 to 4.3 mm) at 90° flexion. At least 2 mm of bony gap discrepancy at 0° extension and 90° flexion was found in 40 patients (67%) and 26 patients (43%), respectively. In terms of femoral bone cut, posterior bone cut thickness was significantly larger than distal bone cut thickness in the medial compartment (p < 0.001). Bony gap discrepancy between distal and posterior regions of the femoral condyle was ≥2 mm in 28 patients (47%). CONCLUSIONS: This study focused on two flaws of mechanically aligned TKA in OA patients. Substantial numbers of patients inevitably required >2 mm of medial collateral ligament release at 0° extension and showed a bone cut discrepancy between distal and posterior regions, carrying a risk of FEA displacement and subsequent unnatural knee motions during knee extension and flexion. Level of evidence IV.