Electron tunneling through self-assembled monolayers (SAMs) composed of either unsaturated or saturated molecules was investigated using conducting probe atomic force microscopy (CP-AFM). SAMs of unsaturated oligophenylene thiolates or saturated alkanethiolates were assembled on Au substrates and contacted with a Au-coated AFM tip at constant applied load. The current-voltage (I-V) characteristics of both types of SAMs were linear over ±0.3 V. Resistance (R) increased exponentially with molecular length (s) in both cases according to the expected relationship, R = R0 exp(βs), but the rate of increase, as quantified by the structure-dependent factor β, was much less for the unsaturated SAMs than for the saturated alkanethiolate SAMs. Average β values were 0.42 ± 0.07 Å-1 for the oligophenylene thiolate SAMs and 0.94 ± 0.06 Å-1 for the alkanethiolate SAMs. Extrapolation of semilog plots of resistance versus molecular length to zero length yielded an estimate of the metal-molecule contact resistance, which was 104 ω for a 50 nm radius Au-coated tip in contact with either the oligophenylene thiolates or alkanethiolates. This study establishes that CP-AFM can be used to probe transport in molecular junctions as a function of molecular dimensions and structure.