Abstract The photorefractive properties of LiNbO3 are closely related to the defect structure which strongly de- pends on the conditions of sample preparation. By means of micro-Raman scattering measurements we investigate the influence of the thermal treatment in the preparation of Fe- diffused waveguides. We underline the role of intrinsic de- fects and discuss the mechanism of incorporation of iron in the lattice. We especially emphasize the specific role of three phonon modes which are able to separately probe the Li, Nb or O sublattice