The influence of the topography of the underlying gold surface on the integrity of self-assembled monolayers (SAMs) of hexadecanethiol (HDT) prepared by solution assembly and microcontact printing was assessed using six different gold substrates. The bare substrates were evaluated for roughness and defects using scanning tunneling microscopy (STM). The structural integrity of self-assembled monolayers on these substrates has been evaluated using both surface methods (STM) and electrochemical measurements. Perhaps not surprisingly, the flattest substrates seem to produce the highest quality monolayer. It is surprising to note, however, that the layer quality is not necessarily traceable to a variation in coverage. Despite both the solution-formed and printed SAMs appearing similar in STM images, electrochemical assessment of the SAM integrity indicated the printed SAMs were inferior, forming a less effective passivating barrier with many more pinholes. The quality of printed SAMs could be improved considerably by rolling the inked stamp across the gold surface rather than placing the stamp horizontally onto the substrate. This second printing technique of rolling the stamp across the surface produced SAMs which were still marginally inferior to those formed from solution but were assembled in less than a minute rather than 24 h.