Exposure to HCl vapor of highly organized self-assembled monolayers (SAMs) of n-alkanoic acids on native oxide-covered Ag, Cu, and Al surfaces results in a variety of structural changes strongly dependent on the specific SAM, Using infrared spectroscopy (IRS) and wetting measurements, it was observed that while SAMs on Al surfaces show no effects of I-ICI exposure over periods of minutes, exposure of SAMs on Ag and Cu over just periods of seconds induces protonation of the carboxylate head groups and severe reorganization of the film into different structural forms of the initial n-alkanoic acid. For the kg SAMs of n-tridecanoic acid (C13) and shorter chains, disordered slates af the acid are produced which upon ambient storage revert back to a carboxylate state with much less order than the initial SAM. However, for C14 and longer chains, protonation occurs to give crystalline forms of the acid. For the C16 SAM, the original structure of all-trans chains, tilted at 19-20 degrees from the surface normal, converts to discreet monoclinic crystallites, estimated from the IRS data to be similar to 5 nm in thickness and oriented with the {010} and/or {001} surface planes parallel to the substrate surface. After 7 days ambient storage. reversion to the original SAM structure occurs, bur for longer chains (e.g., C24) reversal is incomplete. While generally similar results are observed for SAMs on copper, the specific deprotonation and reorganization rates are faster than On Ag and only partial reversibility is observed. These different behaviors are interpreted in terms of a combination of differences in intermolecular interactions, headgroup-substrate interactions, and reactivities of the metal surfaces toward HCl and ambient O-2.