The surface structures of crystals based on aromatic oxadiazoles were investigated by AFM. The crystal structure for 2,5-di(p-tolyl)-1,3,4-oxadiazole (DTO) differs from that of 2,5-di(4-methoxycarbonyl-phenyl)-1,3,4-oxadiazole (DMPO). In DMPO all molecules show parallel orientation to the surface in such a way that the surface is formed as well as by the nitrogen atoms of the heterocyclic rings and the methyl groups of the ester substituents. By contrast, the oxadiazole molecules in DTO crystals are oriented perpendicular to the crystal surface. The experimental data are interpreted by molecular modelling. It is shown that there is a difference between molecular structure of the surface, as detected by AFM, and the bulk structure determined by X-ray diffraction.