The structure of various self-assembled thiol and disulfide monolayers on gold(111) has been studied with the atomic force microscope. The aim was to analyze the factors which determine the two-dimensional structure of the molecules. Monolayers were formed from different disulfides and thiols : long-chain alkyl and perfluoroalkyl esters of bis(2-hydroxyethyl) disulfide, several azobenzenethiols, and octadecanethiol. Three classes of two-dimensional structures could be distinguished : (1) commensurate monolayers, which were dominated by the underlying gold(111) lattice; an example is n-alkanethiol monolayers; (2) incommensurate or at most high-order commensurate monolayers, whose orientation was still determined by the gold(111) substrate; this type of monolayer probably occurred with all disulfides investigated; (3) incommensurate monolayers, whose orientation was arbitrary and not determined by the underlying gold(111). Monolayers of azobenzenthiols belonged to this class.