14-mer alpha-helix and 15-mer beta-strand oligopeptides composed of leucine (L) and lysine (K) were used to investigate peptide adsorption and orientation onto well-defined methyl and carboxylic acid-terminated self-assembled monolayer (SAM) surfaces with X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS). XPS showed that both peptides reached monolayer thickness oil both SAMs, but significantly higher solution concentrations were required to reach this coverage on the methyl SAMs. This shows that the peptides adsorb more strongly onto the carboxyl-terminated SAMs. The excess oxygen detected by XPS and the H3O+ signal detected by ToF-SIMS for the SAMs with adsorbed peptides indicated that water molecules are associated with the adsorbed peptides, even under ultrahigh-vacuum conditions. Changes in the number of L and K fragments detected by ToF-SIMS indicate that the beta-strand oriented differently on the two SAMs. The L side chains were preferentially associated with the methyl-terminated SAM, and the K side chains were preferentially associated with the carboxyl SAM. In contrast, little change in the ToF-SIMS K/L ratio was observed for the alpha-helix peptide absorbed on the two SAMs, indicating that ToF-SIMs was not as sensitive to the orientation of the alpha-helix peptide.