We present a description of the effect of the surface roughness on the energy straggling associated to the energy loss distributions of protons transmitted through a self supported metallic thin foil. For this purpose we prepared a polycrystalline gold thin films using the standard sputtering method with different deposition rates. The statistics of the surface height distribution induced in these thin films were determined using Atomic Force Microscopy. The measured surface roughness allowed us to quantify the ion energy loss straggling in these samples for different deposition parameters and as a function of the incident ion energy.