In this work, we investigated the Schottky barrier height at W/p-type Si contacts with the presence of Ge-dots located below the interface. The effect of the dots is controlled by reducing the thickness of the Si-cap layer by successive chemical oxidation/etching cycles. The surface morphology of the samples is investigated by using atomic force microscopy and the Ge-content is determined by Rutherford backscattering spectroscopy. Nonideal behaviors in current–voltage characteristics are observed and explained in terms of inhomogeneities due to the presence of the Ge-dots.