We present density functional theory calculations of the electronic structure and tunneling characteristics ofalkanethiolate monolayers on Au(111). We systematically analyze root 3 x root 3 full coverage monolayers of SC6H12X molecules with different terminal groups, X = CH3, NH2, SH, OH, COOH, OCH3, on defect-free ("perfect") Au(111). We also study the influence of the surface-molecule bonding structure by comparing the properties of monolayers Of SC6H12CH3 molecules on the perfect surface and on Au(I 11) surfaces with vacancies or adatoms. The tunneling currents (I) through the adsorbed monolayers with a single chemical contact have been calculated within the Tersoff-Hamann approach for voltages between -1 and +1 V. Computed currents are found to depend linearly on V at low voltage, with typical values of similar to 60 and 150 pA/molecule at 0.2 and 0.5 V, respectively, in good agreement with several experimental data. Computed tunneling currents show also a significant dependence on both the terminal group X and the surface structure. In particular, in order of decreasing intensities, currents for the different end groups are NH2 approximate to SH > CH3 > OH > OCH3 > COOK The relationships between the tunneling current, the work function of the surface + SAM, and the lineup of the HOMO with respect to the Fermi energy of the metal surface are examined.