In this work we have compared 125I or 103Pd from a microdosimetric point of view. The photon spectra at different positions around the seeds have first been calculated using EGSnrc Monte Carlo (MC) code. These photon spectra are used as input for the event-by-event MC code TRION to calculate the microdosimetric lineal energy (y) distribution for each isotope. The microdosimetric dose average lineal energy, yD, calculated in a sphere of 1 microm is 3.5 keV microm(-1) for 125I and 4.0 keV microm(-1) for 103Pd, agreeing well with values reported in the literature. yD in a 1 microm sphere diminishes slightly with the distance from the seed for 103Pd. This is due to the spectral hardening caused by the presence of a gamma-ray of 357.5 keV in the initial spectrum of 103Pd. In parallel with the calculation of the microdosimetric spectra, we have analysed the distribution of the size of the energy deposition clusters generated by these low energy photons in structures of 2 and 10 nm of radius. Due to Compton interactions, the fraction of very low energy electrons (<5 keV) generated by 125I photons is 51%, whereas it is only 27% for 103Pd. As these electrons deposit their energy very locally, the pattern of energy depositions contains more clusters of a few nm of radius for 125I than for 103Pd; the mean cluster orders are respectively 3.3 and 3.0 for 10 nm clusters. This is in opposition with the prediction based on the microdosimetric spectrum and the parameter yD and could be of importance for the damage to the cells.