In-situ and ex-situ STM studies of self-assembled butanethiol/Au(111) have been performed in order to determine the ground state configuration and long-term behaviour of this system at room temperature. It is shown that the most stable surface structure is a c(4 x 2) reconstruction of the basic root3 x root3R30degrees adsorption site geometry containing four distinguishable molecules. This structure is extremely sensitive to the presence of defects in the substrate; our results indicate that the formation of the c(4 x 2) superstructure in the butanethiol-Au system is only possible in domains greater than 15-20 nm across (i.e. containing at least 10(3)-10(4) molecules). If the substrate does not present defect-free regions of this size (or greater), nucleation of the c(4 x 2) superstructure is impossible, and the system adopts the simpler root3 x root3R30degrees or pinstripe structure, or the system may remain in a liquid-like state with no apparent local or long-range order. Extended storage and/or manipulation leads to a gradual desorption of adsorbed species and the loss of short-range order in the film spreading out from defect regions, and ultimately leads to the re-configuration of the organic film into a lower coverage p x root3 'pinstripe' structure which is highly stable with respect to further sample manipulation and defects. The sensitivity of the c(4 x 2) structure to the quality of the substrate and sample treatment may be a cause for the widespread perception that short-chain alkanethiol monolayers are intrinsically disordered. (C) 2003 Elsevier B.V. All rights reserved.