The determination of the mechanical stresses induced in human bones is of great importance in both research and clinical practice. Since the stresses in bones cannot be measured non-invasively in vivo, the only way to estimate them is through subject-specific finite element modelling. Several methods exist for the automatic generation of these models from CT data, but before bringing them in the clinical practice it is necessary to assess their accuracy in the predictions of the bone stresses. Particular attention should be paid to those regions, like the epiphyseal and metaphyseal parts of long bones, where the automatic methods are typically less accurate. Aim of the present study was to implement a general procedure to automatically generate subject-specific finite element models of bones from CT data and estimate the accuracy of this general procedure by applying it to one real femur. This femur was tested in vitro under five different loading scenarios and the results of these tests were used to verify how the adoption of a simplified two-material homogeneous model would change the accuracy with respect to the density-based inhomogeneous one, with special attention paid to the epiphyseal and metaphyseal proximal regions of the bone. The results showed that the density-based inhomogeneous model predicts with a very good accuracy the measured stresses (R²=0.91, RMSE=8.6%, peak error=27%), while the two-material model was less accurate (R² = 0.89, RMSE=9.6%, peak error=35%). The results showed that it is possible to automatically generate accurate finite element models of bones from CT data and that the strategy of material properties mapping has a significant influence on its accuracy.