The exchange behavior of various thiol monolayers self-assembled on a gold surface is described. FT-IR external reflection spectroscopy was used for monitoring of the self-exchange of unsubstituted alkanethiol with the aid of deuterated thiol. Intensity changes of the absorption peaks for a specific functionality were used for the quantization of thiols in the monolayers. Exchange of compact monolayers such as eicosanethiol with the same type of alkanethiol in ethanol solution was found to be very slow. We used n-eicosanethiol [CH3(CH2)(19)SH] and partially deuterated eicosanethiol [CD3(CH2)(19)SH] in order to avoid the chain length difference effect of adsorption and maintain exactly the same chain length of molecules. The exchange of the non-compact ferrocene terminated alkanethiol monolayer with dodecanethiol was faster than the self-exchange of the compact unsubstituted alkanethiol monolayer. The result shows that the compactness of the monolayer is critical to the exchange kinetics of self-assembled monolayers.