Innovative methods for morphological and functional analysis of bones have become a primary objective in the development of planning systems for total knee replacement (TKR). These methods involve the interactive identification of clinical landmarks (reference points, distances, angles, and functional axes of movement) and the determination of the optimal implant size and positioning. Among the functional axes used to estimate the correct alignment of the femoral component, the Whiteside line, namely, the anterior-posterior (AP) direction, is one of the most common. In this paper, we present a computational framework that allows automatic identification of the Whiteside line.The approach is based on geometric analysis of the saddle shape of the intercondylar fossa to extract the principal line in the AP direction. A plane parallel to the frontal plane is moved in the AP direction to obtain the 2D profiles of the intercondylar fossa. Each profile is fitted to a fifth-order polynomial curve and its maximum curvature point computed. The point set collected across all the profiles is then processed to compute the principal direction. The 2D profile-fitting and 3D line-fitting residual errors were analyzed to study the relationship between the intercondylar fossa aspect and the nominal saddle surface. The method was validated using femur specimens from elderly subjects reconstructed from CT scans. The repeatability of the method was evaluated across five different femur surface resolutions.For comparison, three expert orthopaedic surgeons identified, by virtual palpation, the Whiteside line on the same 3D femur models. The repeatability (median angular error) of the Whiteside lines computed by the automated method and by manual virtual palpation, was approximately 1.0° and 3.5°, respectively. The angular skew error between the two axes, measured on the axial plane, averaged approximately 4.00° (SD: 2.64°) with no statistical difference. The automated method therefore proved more reproducible and was in agreement with the manual method. We conclude that operator-independent methods, such the one presented in this paper, can be favorably introduced into orthopaedic surgical planning systems.