The assignment of bone tissue material properties is a fundamental step in the generation of subject-specific finite element models from computed tomography data. Aim of the present work is to investigate the influence of the material mapping algorithm on the results predicted by the finite element analysis. Two models, a coarse and a refined one, of a human ileum, femur and tibia, were generated from CT data and used for the tests. In addition a convergence analysis was carried out for the femur model, using six refinement levels, to verify whether the inclusion of the material properties would significantly alter the convergence behaviour of the mesh. The results showed that the choice of the mapping algorithm influences the material distribution. However, this did not always propagate into the finite element results. The difference between the maximum Von Mises stress remained always lower than 10%, apart one case when it reached the 13%. However, the global behaviour of the meshes showed more marked differences between the two algorithms: in the finer meshes of the two long bones 20-30% of the bone volume showed differences in the predicted Von Mises stresses greater than 10%. The convergence behaviour of the model was not worsened by the introduction of inhomogeneous material properties. The software was made available in the public domain.