The surface structure of dodecanethiolate self-assembled monolayers (SAMs) on Au(111) surfaces, formed from the liquid phase, have been studied by grazing incidence X-ray diffraction (GIXRD), scanning tunneling microscopy (STM), and electrochemical techniques. STM images show that the surface structure consists of (square root 3 x square root 3)-R30 degrees domains with only a few domains of the c(4 x 2) lattice. The best fitting of GIXRD data for the (square root 3 x square root 3)-R30 degrees lattice is obtained with alkanethiolate adsorption at the top sites, although good fittings are also obtained for the fcc and hcp hollow sites. On the basis of this observation, STM data, electrochemical measurements, and previously reported data, we propose a two-site model that implies the formation of incoherent domains of alkanethiolate molecules at top and fcc hollow sites. This model largely improves the fitting of the GIXRD data with respect to those observed for single adsorption sites and, also, for the other possible two-site combinations. The presence of alkanethiolate molecules adsorbed at the less favorable top sites could result from the adsorption pathway that involves an initial physisorption step which, for steric reasons, takes place at on top sites. Once the molecules are chemisorbed, the presence of energy barriers for alkanethiolate surface diffusion, arising mostly from chain-chain interactions, "freezes" some of them at the on top sites, hindering their movement toward fcc hollow sites. By considering the length of the hydrocarbon chain and the adsorption time, the two-site model could be a tool to explain most of the controversial results on this matter reported in the literature.