Silicon (Si) has been the most widely used semiconductor for decades, playing an important role in the field of electronics, energy conversion and energy storage. Because of their unique morphological energy band characteristics, Si nanostructures exhibit superior performance in many applications in comparison with their bulk counterparts. In this study, the effects of thermal annealing on elemental composition and morphological properties of palladium metal thin films grown on c-Si substrates were investigated. Palladium (Pd) thin films of different thicknesses were deposited on Si (1 0 0) with and without native oxide layers by electron beam evaporation and annealed in vacuum at 600 °C for two hours. Scanning electron microscopy (SEM) studies have shown that the surface morphology showed an effective dewetting in individual droplets and islands which further coalesce into bigger islands. Rutherford backscattering spectrometry (RBS) and electrical measurements analyses revealed the diffusion of the Si substrate into the Pd layer during annealing. This contribution will discuss the effects of the metal layer thickness as well as the native oxide on the metal thin films.