Molecular dynamics simulations were performed to study friction in self-assembled monolayers of alkanethiols on gold. The simulations yield a Frictional force that is proportional to the applied load, consistent with Amontons’ second law for macroscopic systems. It is further demonstrated that the chain length of the alkanethiols and the load under which the surfaces interact has an effect on the structure of the monolayer film during compression. The simulations suggest, however, that these changes in structure have little effect on the friction properties of the monolayer film. Also, the mode of energy dissipation in both this system and a system in which two monolayer films interact is examined.