The structures of vapour deposited layers of adenine on a nanostructured SrTiO3(001) surface have been investigated by scanning tunneling microscopy (STM). The STM images reveal details of self-organization of adenine monolayers in which adsorption is controlled both by substrate nanostructure and by intermolecular H-bonding of adenine molecules. Detailed examination of STM images suggests that at least three different ordering structures are possible and two distinct orientations may exist with opposite chirality