Frequently, when growing III-V semiconductors on germanium substrates, unexpected differences between nominally identical substrates are encountered. Using atomic force microscopy (AFM), we have analysed a set of germanium substrates sharing the same specifications. The substrates come from the same vendor but different results come about in terms of the morphology of the epilayers produced by the same epitaxial routine (i.e. substrate W1 produced epilayers with good morphology while substrate WX produced epilayers with defects). The morphological analysis has been carried out on (a) epiready substrates; (b) samples after a high-temperature bake at 700 degrees C; and (c) on the samples after a hydride (PH3) annealing at 640 degrees C. In the two first stages all substrates (both W1 and WX) show the same good morphology with RMS roughness below 3 A in all cases. It is in the third stage (annealing in PH3) that the morphology degrades and the differences between the samples become apparent. After phosphine exposure at 640 degrees C, the RMS roughness of both substrates approximately doubles. and their surface appears as full of peaks and valleys on the nanometre scale. Despite the general appearance of the samples being similar, a careful analysis of their Surface reveals that the substrates that produce bad morphologies (WX) show higher peaks, and some of their roughness parameters, namely, surface kurtosis and the surface skewness, are considerably degraded. (C) 2008 Elsevier B.V. All rights reserved.