The dosimetric dependence of the bone and lung heterogeneities with the dose in water was evaluated using two photon beam energies (300 kVp and 225 kVp) and two field sizes for the X-RAD 320 preclinical irradiator by Monte Carlo simulations using the code DOSXYZnrc from a point source of isotropic radiation that emits energy spectra generated with the SpekCalc program. This was carried out in two water phantoms to which bone and lung heterogeneities were introduced respectively and for a computational mouse phantom generated from simulations with the MOBY program. A significant increase in the dose in bone was found when photon beams of 300 and 225 kVp were used, this effect is greater as the energy decreases. This dosimetric effect, due to the presence of bone heterogeneity, was more significant compared to lung heterogeneity. Therefore, for kV photon energies in the range used in irradiating small animals, increasing the dose to bone due to the photoelectric effect could be a dosimetric concern.