In recent years, optical techniques based on diffusion approximation have demonstrated their ability to gain rich spectral information about bone. However, these methods normally assume homogeneity, while cancellous bone and marrow form a highly heterogeneous two-phase medium. This paper studies the limitations of this assumption, and quantifies the role of microstructure on long-range transport properties. The propagation of light pulses through trabecular bone is calculated by Monte Carlo simulation of the scattering and absorption in reconstructions of bone samples obtained from x-ray micro tomographic scans. The time-resolved responses are then fitted with the analytical response of a homogeneous material to obtain the apparent transport properties. These properties are used to test different homogenization equations that have been postulated in the past for heterogeneous tissues and to check their accuracy. The results show that nonlinearity and crosstalk between absorption and scattering are statistically significant, although their impact is relatively small. More importantly, we found that the weight of the components is not only affected by their volume fractions, but need to be corrected by other morphologic measures like trabecular spacing or connectivity density. These deviations from the homogeneous assumption are stronger for scattering than for absorption. In conclusion, the average optical properties of cancellous bone are strongly determined by its microstructure, meaning that optical techniques are a valid method for tissue evaluation, but careful consideration of structurerelated perturbation sources is required.