In order to find factors which determine the two-dimensional structure of self-assembled monolayers (SAMs), several classes of thiols and disulfides on gold (111) have been investigated by atomic force microscopy (AFM). SAMs were formed from a series of symmetrical and asymmetrical diethylalkanoate disulfides, omega-hydroxy-and omega-carboxyalkanethiols, diacetylene disulfides, and different anthracene terminated thiols and disulfides. In all the cases, two-dimensional crystalline structures could be resolved; even for an asymmetrical diethylalkanoate disulfide that had a chain length difference of five methylene units. The lattices were analyzed quantitatively. Two distinctly different types of crystalline structures were observed, namely, a hexagonal and a centered rectangular lattice. For the diethylalkanoate disulfides with short alkyl chains (n less than or equal to 10) both structural phases were observed, domains with a hexagonal lattice existing simultaneously with centered rectangular domains. The lenth of the alkyl chain determined the probability of finding disulfides in the hexagonal structure. This dependence on the shape of the molecules as well as the clear contrast of SAMs of asymmetric disulfides suggest that the AFM tip penetrates into the SAMs and probes, at least partially, the interior of the layers. With the atomic force microscope no difference was observed between SAMs formed from thiols and those from disulfides.