The rich topography of a self-assembled monolayer formed by a helical hexapeptide chemisorbed on a gold surface has been investigated by scanning tunneling microscopy under ultra high vacuum conditions (UHV–STM). STM experiments revealed a complex morphology of the peptide layer, showing nanometric-ordered domains lying on the gold surface (stripes) and a predominant phase at high local peptide concentration (holes). Diffusion of gold–peptide adsorbates on the gold surface, leading to coalescence of the hole structures at room temperature, was also detected.