Shape-from-focus (SFF) has widely been studied in computer vision as a passive depth recovery and 3D reconstruction method. One of the main stages in SFF is the computation of the focus level for every pixel of an image by means of a focus measure operator. In this work, a methodology to compare the performance of different focus measure operators for shape-from-focus is presented and applied. The selected operators have been chosen from an extensive review of the state-of-the-art. The performance of the different operators has been assessed through experiments carried out under different conditions, such as image noise level, contrast, saturation and window size. Such performance is discussed in terms of the working principles of the analyzed operators.