The synthesis and characterization of long-chain alkyltrichlorosilanes of alkyl halides, benzyl halides, and α-haloacetyls designed to form siloxane-anchored self-assembled monolayers (SAMs) for the selective attachment of peptides (via cysteine thiols) is described. Thin film formation by the trichlorosilanes was demonstrated by spectroscopic means and by surface wetting properties. Halide exchange could be utilized to produce the more reactive (iodide) surfaces in situ, following their deposition in a more stable (chloride or bromide) form. In solution, these functional groups were found to have a range of reactivity with model thiols which extended from half-lives of minutes to days (essentially no reactivity). The order of reactivity is I > Br > Cl within each class of compounds, and α-haloacetyl > benzyl ≫ alkyl. The reactivity of the SAMs with thiols showed the same order of reactivity. The very reactive α-iodoacetyl was also reactive with amines, but competition experiments demonstrated preference for the thiol under our reaction conditions. SAM reactivity with cysteine-containing peptides was demonstrated with a tripeptide (glutathione) and a nonapeptide (laminin fragment). Both peptides show maximum attachment after 2–3 h of exposure to millimolar concentrations. The attachment was completely blocked by prior treatment of these peptides with dinitrophenylmaleimide or by air oxidation of the thiol. Given that these peptides contain all the nucleophilic side chains found in proteins (thiol, alcohol, phenol, carboxyl, and amine), the selective blocking experiments indicate that these SAMs will be useful for the directed attachment through cysteine side chains in proteins and peptides.