The (001) surface of a single crystal of guanidinium methanesulfonate, which has a bilayer architecture, has been investigated and characterized by He diffraction in the temperature range between 40 and 100 K. The goal of these studies was to demonstrate that the surface structure of a single crystal could be determined by He diffraction and to identify the preferred cleavage plane in these crystals. The measured periodicity on different cleaved samples was consistent with the structure of the (001) plane as determined by previous single-crystal X-ray diffraction, The data, however, indicated that cleavage produced a surface terminated either by hydrogen-bonded guanidinium sulfonate sheets or by methyl groups projecting outward from these sheets. These different surfaces afforded slightly different He diffraction patterns along with different rates of decay in the thermal attenuation of the elastic scattered intensities. In particular, only one of the rates shows a dependence on the parallel momentum exchange, which is similar to that measured for self-assembled monolayers of alkanethiols on Au(111). These results suggest that He diffraction is sufficiently sensitive for distinguishing between the two possible (001) cleavage planes.