Auger in-depth profiles were measured on a Mo-Si multilayer structure, consisting of 45 periods of 3.3 nm molybdenum and 3.6 nm silicon layers, by means of Ar ion bombardment with rotated specimen and a glancing incidence ion beam probe. The relative sputtering yield of Si and Mo is determined in the ranges of 2-6 keV ion energy and 80-degrees-87-degrees incidence angle with respect to the surface normal. It is shown that the depth resolution depends strongly on the ion energy. The depth resolution changes immediately when the ion energy is changed. This observation is explained by the fact that the depth resolution in our experiment is limited by ion mixing and not by surface roughening. Attempts to determine the initial structure from the measured profile through application of Liau’s model on ion sputtering were not completely successful.