We report a static secondary ion mass spectrometry (SSIMS) study of self-assembled monolayers (SAMs) of alkanethiols [CH3(CH2)nSH, where n = 7, 9, 11, 15, 17] adsorbed on Au. A rich variety of molecular secondary ions are observed in the negative SSIMS spectra including (M - H)-, (AuM)-, (AuSM)-, and (Au2[M - H])- and a relatively strong (Au[M - H]2)- where M is the complete alkanethiol molecule. Sulfonates and alkanesulfonates are observed in SSIMS spectra of SAMs that have been atmosphere exposed for prolonged periods; however, sulfonate species are not detected from samples that are analyzed immediately after withdrawal from thiol-ethanol solutions. SSIMS results indicate that sulfonates formed by air oxidation can be displaced by reimmersion of samples in thiol adsorbate solution. Molecular secondary ions are not observed for perfluoromercaptan and carboxylic acid-terminated SAMs, although spectra distinct from those of the alkanethiol SAMs were obtained. Damage profiles indicate that the emission of molecular secondary ions is very sensitive to extremely low primary ion beam doses. In addition, the relative intensities of Au substrate and molecular ions are strongly influenced by the energy of the primary ion beam suggesting a beam penetration depth effect.