High-resolution electron energy loss spectroscopy (HREELS) was used tb investigate the molecular structure of self-assembled monolayers formed by adsorption of n-alkanethiols, alpha,omega-alkanedithiols, and alpha-cycloalkyl-omega-alkanethiols on different gold substrates. The HREELS data are reported as a contribution to a general effort to assess the potential of electron spectroscopies in the elucidation of structural characteristics of organic surfaces. Typical fingerprints of the thiol molecules, characteristic of their primary and secondary structure (connectivity, conformation, and order), have been found in their HREELS vibrational spectra. We have shown that when the layers are disordered, the spectra are dominated by impact-excited modes, hampering the identification of the compounds. These data have evidenced many defects in the organization of the monolayers on evaporated gold substrates. The coherent domains sizes formed by the molecules in the films have been estimated from the angular distribution of the elastic peak as a function of the nature of the alkanethiol chain and of the immersion time in thiol solutions.