The effect of thermal annealing on the structural properties of electron beam evaporated polycrystalline Si/Ge multilayer structures has been studied using Grazing incidence X-ray diffraction (GIXRD), reflectivity (GIXRR) and Raman spectroscopy techniques. The chemical nature of layers at surface and interfaces has been obtained from X-ray photoelectron spectroscopy (XPS) technique, which revealed the presence of impurities only at the top surface in the form of carbides and oxides in the Si layer and in elemental form in the Ge layer. Reflectivity measurements show that the Si/Ge MLS is stable upto 200 °C and roughness of Si on Ge interface is higher as compared to that of Ge on Si interface. Similarly, GIXRD results show that upto 200 °C, MLS is of microcrystalline nature and further annealing at 300 °C and 400 °C, well-defined crystalline peaks of pure Si and Ge are observed, which is in contrast to earlier reported experimental findings. Observed results are interpreted in terms of diffusion induced crystallization and corresponding increase in grain size.