The interaction of ferrocene- 1, 1' -dithiol (FDT) with two parallel Ag(111) surfaces has been theoretically studied at density-functional level. The effect of surface defects on the energetic and electronic structure was investigated. The electronic transport properties are studied with the nonequilibrium Green's function approach. The adsorption geometry has a strong effect on the electronic levels and conductivity. The presence of point defects strongly enhances the molecule-surface interaction but has a surprisingly small effect on the density of states near the Fermi energy. The FDT-surface bond is particularly strong near terraces or steps and leads to significant shifts of the molecular orbitals relative to the gas phase. For all considered defect types except the single adatom the electronic conductivity through the FDT molecule is decreased compared to adsorption on perfect surfaces. © 2008 American Institute of Physics.