The Fast Fourier Transform-based method, originally introduced by Moulinec and Suquet in 1994 has gained popularity for computing homogenized properties of composites. In this work, the method is used for the computational homogenization of the elastic properties of cancellous bone. To the authors' knowledge, this is the first study where the Fast Fourier Transform scheme is applied to bone mechanics. The performance of the method is analyzed for artificial and natural bone samples of 2 species: bovine femoral heads and implanted femurs of Hokkaido rats. Model geometries are constructed using data from X-ray tomographies, and the bone tissue elastic properties are measured using microindentation and nanoindentation tests. Computed results are in excellent agreement with those available in the literature. The study shows the suitability of the method to accurately estimate the fully anisotropic elastic response of cancellous bone. Guidelines are provided for the construction of the models and the setting of the algorithm.