A simple approach to the in situ measurement of infrared spectra of self-assembled monolayers (SAMs) on gold in an aqueous environment is described. A thin gold film (3-5 nm) on the surface of a germanium internal reflection element is used as a substrate for the self-assembly of a monolayer of a chelating thioalkane. High signal-to-noise spectra are obtained, allowing identification of the chemical groups present in the SAM. Complexation of ions by the SAM can be monitored, and the secondary conformation of his-tagged proteins bound to the SAM can be observed.