We have performed a comparative study of oxide- and nonoxide-passivated silicon nanocrystals to probe the role of the silicon/oxygen interface in low coverage, non-interacting silicon nanocrystal systems. Ensembles of Si nanocrystals characterized by a narrow distribution and diameters of 2–5 nm were synthesized by ion implantation into SiO2 films followed by a high-temperature anneal in Ar. The nanocrystals were removed from the SiO2 film matrix and deposited on Si substrates using a chemical etch in HF, leaving a hydrogen-terminated surface. A natural oxide layer grows on these surfaces in air. We characterized the morphology of the samples with atomic force microscopy (AFM) and the spectroscopic properties with photoluminescence (PL) and X-Ray photoelectron spectroscopy. We found that the PL energy of Si nanocrystals can be shifted by particle size reduction and hydrogen or oxygen termination. Further, PL peak energy shifts upon etching and oxidation were consistent with the model of Wolkin et al. that proposes that for very small radii, a silicon-oxygen double bond will produce deep interface states which red shift the luminescence.