The importance of metal-molecule interfaces in determining the current-voltage (I-V) characteristics of molecular junctions has been made clear in theoretical work over the past 5 years. Yet systematic experimental investigations, in which the contact effects are mapped out as a function of the metal work function and the type of surface linker used to bind the molecules to the electrodes, have not been carried out. This talk describes a conducting probe atomic force microscopy (CP-AFM) approach to the experimental examination of contact effects in molecular junctions. Junctions are fabricated by contacting self-assembled monolayers (SAMs) on metal substrates with metal-coated AFM tips; it is possible to contact SAMs with any metal that can be coated onto an AFM tip. Contact resistances are estimated by measuring total junction resistance (at different bias voltages) as a function of the length of the molecules between the tip and substrate contacts, and then extrapolating resistance versus length plots to zero length. We find that contact resistances in molecular junctions are sensitive to the metal work function, the type of surface linker (e.g., -SH vs –NC), and the bonding in the molecular backbone (i.e., conjugated vs saturated). Importantly, the work function dependence allows qualitative estimation of where the Fermi level of the junction lies with respect to the HOMO and LUMO of the molecules. We will summarize our findings to date on contact effects in junctions composed of molecules with alkane or oligophenylene backbones.