Tuning the charge transport through a metal-molecule-metal junction by changing the interface properties is widely studied and is of paramount importance for applications in molecular electronic devices. We used current sensing atomic force microscopy (CSAFM) as a tool to study the contact resistance of metal-molecule-metal (MmM) junctions formed by sandwiching self-assembled monolayers (SAMs) of alkanethiols with various end groups (-CH3, -OH and -NH2) between Au(111) substrates and An coated AFM tips. The effect of interface chemistry on charge transport through such SAMs with varying end groups was studied in an inert, non-polar liquid (hexadecane) environment. We find that the contact resistances of these MmM junctions vary significantly based on the end group chemistry of the molecules. (c) 2005 Elsevier B.V. All rights reserved.